diff --git "a/annotation_CSV/PMC4854314.csv" "b/annotation_CSV/PMC4854314.csv"
new file mode 100644--- /dev/null
+++ "b/annotation_CSV/PMC4854314.csv"
@@ -0,0 +1,472 @@
+anno_start	anno_end	anno_text	entity_type	sentence	section
+0	3	RNA	chemical	RNA protects a nucleoprotein complex against radiation damage	TITLE
+15	28	nucleoprotein	complex_assembly	RNA protects a nucleoprotein complex against radiation damage	TITLE
+49	60	protein–RNA	complex_assembly	Systematic analysis of radiation damage within a protein–RNA complex over a large dose range (1.3–25 MGy) reveals significant differential susceptibility of RNA and protein.	ABSTRACT
+157	160	RNA	chemical	Systematic analysis of radiation damage within a protein–RNA complex over a large dose range (1.3–25 MGy) reveals significant differential susceptibility of RNA and protein.	ABSTRACT
+16	58	difference electron-density quantification	experimental_method	A new method of difference electron-density quantification is presented.	ABSTRACT
+24	77	macromolecular X-ray crystallographic data collection	experimental_method	Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations.	ABSTRACT
+116	155	macromolecular structure determinations	experimental_method	Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations.	ABSTRACT
+57	65	crystals	evidence	Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes.	ABSTRACT
+47	71	per-atom density changes	evidence	Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3–25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein–DNA complex.	ABSTRACT
+244	247	DNA	chemical	Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3–25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein–DNA complex.	ABSTRACT
+64	99	trp RNA-binding attenuation protein	protein_type	Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein.	ABSTRACT
+101	105	TRAP	complex_assembly	Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein.	ABSTRACT
+107	115	bound to	protein_state	Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein.	ABSTRACT
+134	137	RNA	chemical	Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein.	ABSTRACT
+29	32	RNA	chemical	Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein.	ABSTRACT
+24	28	TRAP	complex_assembly	The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility.	ABSTRACT
+91	96	bound	protein_state	The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility.	ABSTRACT
+97	100	RNA	chemical	The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility.	ABSTRACT
+160	163	RNA	chemical	The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility.	ABSTRACT
+33	37	TRAP	complex_assembly	The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule.	ABSTRACT
+38	42	ring	structure_element	The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule.	ABSTRACT
+95	98	Glu	residue_name	The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule.	ABSTRACT
+103	106	Asp	residue_name	The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule.	ABSTRACT
+129	132	RNA	chemical	The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule.	ABSTRACT
+236	255	RNA-binding pockets	site	The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule.	ABSTRACT
+88	91	Lys	residue_name	Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.	ABSTRACT
+96	99	Phe	residue_name	Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.	ABSTRACT
+117	120	RNA	chemical	Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.	ABSTRACT
+147	163	electron density	evidence	Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.	ABSTRACT
+150	173	structure determination	experimental_method	With the wide use of high-flux third-generation synchrotron sources, radiation damage (RD) has once again become a dominant reason for the failure of structure determination using macromolecular crystallography (MX) in experiments conducted both at room temperature and under cryocooled conditions (100 K).	INTRO
+180	210	macromolecular crystallography	experimental_method	With the wide use of high-flux third-generation synchrotron sources, radiation damage (RD) has once again become a dominant reason for the failure of structure determination using macromolecular crystallography (MX) in experiments conducted both at room temperature and under cryocooled conditions (100 K).	INTRO
+212	214	MX	experimental_method	With the wide use of high-flux third-generation synchrotron sources, radiation damage (RD) has once again become a dominant reason for the failure of structure determination using macromolecular crystallography (MX) in experiments conducted both at room temperature and under cryocooled conditions (100 K).	INTRO
+133	141	crystals	evidence	Significant progress has been made in recent years in understanding the inevitable manifestations of X-ray-induced RD within protein crystals, and there is now a body of literature on possible strategies to mitigate the effects of RD (e.g. Zeldin, Brockhauser et al., 2013; Bourenkov & Popov, 2010).	INTRO
+91	93	MX	experimental_method	However, there is still no general consensus within the field on how to minimize RD during MX data collection, and debates on the dependence of RD progression on incident X-ray energy (Shimizu et al., 2007; Liebschner et al., 2015) and the efficacy of radical scavengers (Allan et al., 2013) have yet to be resolved.	INTRO
+140	159	diffraction pattern	evidence	Global radiation damage is observed within reciprocal space as the overall decay of the summed intensity of reflections detected within the diffraction pattern as dose increases (Garman, 2010; Murray & Garman, 2002).	INTRO
+174	176	MX	experimental_method	Dose is defined as the absorbed energy per unit mass of crystal in grays (Gy; 1 Gy = 1 J kg−1), and is the metric against which damage progression should be monitored during MX data collection, as opposed to time.	INTRO
+158	165	crystal	evidence	At 100 K, an experimental dose limit of 30 MGy has been recommended as an upper limit beyond which the biological information derived from any macromolecular crystal may be compromised (Owen et al., 2006).	INTRO
+1	26	Specific radiation damage	experimental_method	 Specific radiation damage (SRD) is observed in the real-space electron density, and has been detected at much lower doses than any observable decay in the intensity of reflections.	INTRO
+28	31	SRD	experimental_method	 Specific radiation damage (SRD) is observed in the real-space electron density, and has been detected at much lower doses than any observable decay in the intensity of reflections.	INTRO
+52	79	real-space electron density	evidence	 Specific radiation damage (SRD) is observed in the real-space electron density, and has been detected at much lower doses than any observable decay in the intensity of reflections.	INTRO
+14	16	Se	chemical	Indeed, the C—Se bond in selenomethionine, the stability of which is key for the success of experimental phasing methods, can be cleaved at a dose as low as 2 MGy for a crystal maintained at 100 K (Holton, 2007).	INTRO
+25	41	selenomethionine	chemical	Indeed, the C—Se bond in selenomethionine, the stability of which is key for the success of experimental phasing methods, can be cleaved at a dose as low as 2 MGy for a crystal maintained at 100 K (Holton, 2007).	INTRO
+169	176	crystal	evidence	Indeed, the C—Se bond in selenomethionine, the stability of which is key for the success of experimental phasing methods, can be cleaved at a dose as low as 2 MGy for a crystal maintained at 100 K (Holton, 2007).	INTRO
+132	146	disulfide-bond	ptm	SRD has been well characterized in a large range of proteins, and is seen to follow a reproducible order: metallo-centre reduction, disulfide-bond cleavage, acidic residue decarboxylation and methionine methylthio cleavage (Ravelli & McSweeney, 2000; Burmeister, 2000; Weik et al., 2000; Yano et al., 2005).	INTRO
+112	125	MX-determined	experimental_method	There are a number of cases where SRD manifestations have compromised the biological information extracted from MX-determined structures at much lower doses than the recommended 30 MGy limit, leading to false structural interpretations of protein mechanisms.	INTRO
+126	136	structures	evidence	There are a number of cases where SRD manifestations have compromised the biological information extracted from MX-determined structures at much lower doses than the recommended 30 MGy limit, leading to false structural interpretations of protein mechanisms.	INTRO
+0	20	Active-site residues	site	Active-site residues appear to be particularly susceptible, particularly for photosensitive proteins and in instances where chemical strain is an intrinsic feature of the reaction mechanism.	INTRO
+14	37	structure determination	experimental_method	For instance, structure determination of the purple membrane protein bacterio­rhodopsin required careful corrections for radiation-induced structural changes before the correct photosensitive intermediate states could be isolated (Matsui et al., 2002).	INTRO
+69	87	bacterio­rhodopsin	protein_type	For instance, structure determination of the purple membrane protein bacterio­rhodopsin required careful corrections for radiation-induced structural changes before the correct photosensitive intermediate states could be isolated (Matsui et al., 2002).	INTRO
+66	77	active site	site	The significant chemical strain required for catalysis within the active site of phosphoserine aminotransferase has been observed to diminish during X-ray exposure (Dubnovitsky et al., 2005).	INTRO
+81	111	phosphoserine aminotransferase	protein_type	The significant chemical strain required for catalysis within the active site of phosphoserine aminotransferase has been observed to diminish during X-ray exposure (Dubnovitsky et al., 2005).	INTRO
+22	33	SRD studies	experimental_method	Since the majority of SRD studies to date have focused on proteins, much less is known about the effects of X-ray irradiation on the wider class of crystalline nucleoprotein complexes or how to correct for such radiation-induced structural changes.	INTRO
+160	173	nucleoprotein	complex_assembly	Since the majority of SRD studies to date have focused on proteins, much less is known about the effects of X-ray irradiation on the wider class of crystalline nucleoprotein complexes or how to correct for such radiation-induced structural changes.	INTRO
+53	56	DNA	chemical	Understanding RD to such complexes is crucial, since DNA is rarely naked within a cell, instead dynamically interacting with proteins, facilitating replication, transcription, modification and DNA repair.	INTRO
+193	196	DNA	chemical	Understanding RD to such complexes is crucial, since DNA is rarely naked within a cell, instead dynamically interacting with proteins, facilitating replication, transcription, modification and DNA repair.	INTRO
+24	37	nucleoprotein	complex_assembly	As of early 2016, >5400 nucleoprotein complex structures have been deposited within the PDB, with 91% solved by MX.	INTRO
+46	56	structures	evidence	As of early 2016, >5400 nucleoprotein complex structures have been deposited within the PDB, with 91% solved by MX.	INTRO
+112	114	MX	experimental_method	As of early 2016, >5400 nucleoprotein complex structures have been deposited within the PDB, with 91% solved by MX.	INTRO
+76	86	structures	evidence	It is essential to understand how these increasingly complex macromolecular structures are affected by the radiation used to solve them.	INTRO
+0	14	Nucleoproteins	complex_assembly	Nucleoproteins also represent one of the main targets of radiotherapy, and an insight into the damage mechanisms induced by X-ray irradiation could inform innovative treatments.	INTRO
+198	201	DNA	chemical	Investigations on sub-ionization-level LEEs (0–15 eV) interacting with both dried and aqueous oligonucleotides (Alizadeh & Sanche, 2014; Simons, 2006) concluded that resonant electron attachment to DNA bases and the sugar-phosphate backbone could lead to the preferential cleavage of strong (∼4 eV, 385 kJ mol−1) sugar-phosphate C—O covalent bonds within the DNA backbone and then base-sugar N1—C bonds, eventually leading to single-strand breakages (SSBs; Ptasińska & Sanche, 2007).	INTRO
+359	362	DNA	chemical	Investigations on sub-ionization-level LEEs (0–15 eV) interacting with both dried and aqueous oligonucleotides (Alizadeh & Sanche, 2014; Simons, 2006) concluded that resonant electron attachment to DNA bases and the sugar-phosphate backbone could lead to the preferential cleavage of strong (∼4 eV, 385 kJ mol−1) sugar-phosphate C—O covalent bonds within the DNA backbone and then base-sugar N1—C bonds, eventually leading to single-strand breakages (SSBs; Ptasińska & Sanche, 2007).	INTRO
+50	86	electron spin resonance spectroscopy	experimental_method	Electrons have been shown to be mobile at 77 K by electron spin resonance spectroscopy studies (Symons, 1997; Jones et al., 1987), with rapid electron quantum tunnelling and positive hole migration along the protein backbone and through stacked DNA bases indicated as a dominant mechanism by which oxidative and reductive damage localizes at distances from initial ionization sites at 100 K (O’Neill et al., 2002).	INTRO
+245	248	DNA	chemical	Electrons have been shown to be mobile at 77 K by electron spin resonance spectroscopy studies (Symons, 1997; Jones et al., 1987), with rapid electron quantum tunnelling and positive hole migration along the protein backbone and through stacked DNA bases indicated as a dominant mechanism by which oxidative and reductive damage localizes at distances from initial ionization sites at 100 K (O’Neill et al., 2002).	INTRO
+365	381	ionization sites	site	Electrons have been shown to be mobile at 77 K by electron spin resonance spectroscopy studies (Symons, 1997; Jones et al., 1987), with rapid electron quantum tunnelling and positive hole migration along the protein backbone and through stacked DNA bases indicated as a dominant mechanism by which oxidative and reductive damage localizes at distances from initial ionization sites at 100 K (O’Neill et al., 2002).	INTRO
+187	199	crystallized	experimental_method	The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015).	INTRO
+247	256	bacterial	taxonomy_domain	The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015).	INTRO
+265	268	DNA	chemical	The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015).	INTRO
+278	288	C.Esp1396I	complex_assembly	The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015).	INTRO
+460	463	DNA	chemical	The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015).	INTRO
+475	482	crystal	evidence	The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015).	INTRO
+91	106	AT-rich regions	structure_element	Only at doses above 20 MGy were precursors of phosphodiester-bond cleavage observed within AT-rich regions of the 35-mer DNA.	INTRO
+121	124	DNA	chemical	Only at doses above 20 MGy were precursors of phosphodiester-bond cleavage observed within AT-rich regions of the 35-mer DNA.	INTRO
+34	44	C.Esp1396I	complex_assembly	For crystalline complexes such as C.Esp1396I, whether the protein is intrinsically more susceptible to X-ray-induced damage or whether the protein scavenges electrons to protect the DNA remains unclear in the absence of a non-nucleic acid-bound protein control obtained under exactly the same crystallization and data-collection conditions.	INTRO
+182	185	DNA	chemical	For crystalline complexes such as C.Esp1396I, whether the protein is intrinsically more susceptible to X-ray-induced damage or whether the protein scavenges electrons to protect the DNA remains unclear in the absence of a non-nucleic acid-bound protein control obtained under exactly the same crystallization and data-collection conditions.	INTRO
+83	90	crystal	evidence	To monitor the effects of nucleic acid binding on protein damage susceptibility, a crystal containing two protein molecules per asymmetric unit, only one of which was bound to RNA, is reported here (Fig. 1 ▸).	INTRO
+167	175	bound to	protein_state	To monitor the effects of nucleic acid binding on protein damage susceptibility, a crystal containing two protein molecules per asymmetric unit, only one of which was bound to RNA, is reported here (Fig. 1 ▸).	INTRO
+176	179	RNA	chemical	To monitor the effects of nucleic acid binding on protein damage susceptibility, a crystal containing two protein molecules per asymmetric unit, only one of which was bound to RNA, is reported here (Fig. 1 ▸).	INTRO
+48	62	controlled SRD	experimental_method	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+134	145	protein–RNA	complex_assembly	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+155	190	trp RNA-binding attenuation protein	protein_type	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+192	196	TRAP	complex_assembly	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+198	206	bound to	protein_state	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+215	218	RNA	chemical	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+228	240	(GAGUU)10GAG	chemical	Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002).	INTRO
+0	4	TRAP	complex_assembly	TRAP consists of 11 identical subunits assembled into a ring with 11-fold rotational symmetry.	INTRO
+30	38	subunits	structure_element	TRAP consists of 11 identical subunits assembled into a ring with 11-fold rotational symmetry.	INTRO
+56	60	ring	structure_element	TRAP consists of 11 identical subunits assembled into a ring with 11-fold rotational symmetry.	INTRO
+29	32	K d	evidence	It binds with high affinity (K d ��� 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999).	INTRO
+46	49	RNA	chemical	It binds with high affinity (K d ≃ 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999).	INTRO
+73	89	GAG/UAG triplets	structure_element	It binds with high affinity (K d ≃ 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999).	INTRO
+116	134	spacer nucleotides	structure_element	It binds with high affinity (K d ≃ 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999).	INTRO
+191	201	tryptophan	chemical	It binds with high affinity (K d ≃ 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999).	INTRO
+224	241	Bacillus subtilis	species	It binds with high affinity (K d ≃ 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999).	INTRO
+8	17	structure	evidence	In this structure, the bases of the G1-A2-G3 nucleotides form direct hydrogen bonds to the protein, unlike the U4-U5 nucleotides, which appear to be more flexible.	INTRO
+36	44	G1-A2-G3	chemical	In this structure, the bases of the G1-A2-G3 nucleotides form direct hydrogen bonds to the protein, unlike the U4-U5 nucleotides, which appear to be more flexible.	INTRO
+111	116	U4-U5	chemical	In this structure, the bases of the G1-A2-G3 nucleotides form direct hydrogen bonds to the protein, unlike the U4-U5 nucleotides, which appear to be more flexible.	INTRO
+33	35	MX	experimental_method	Ten successive 1.98 Å resolution MX data sets were collected from the same TRAP–RNA crystal to analyse X-ray-induced structural changes over a large dose range (d 1 = 1.3 MGy to d 10 = 25.0 MGy).	INTRO
+75	83	TRAP–RNA	complex_assembly	Ten successive 1.98 Å resolution MX data sets were collected from the same TRAP–RNA crystal to analyse X-ray-induced structural changes over a large dose range (d 1 = 1.3 MGy to d 10 = 25.0 MGy).	INTRO
+84	91	crystal	evidence	Ten successive 1.98 Å resolution MX data sets were collected from the same TRAP–RNA crystal to analyse X-ray-induced structural changes over a large dose range (d 1 = 1.3 MGy to d 10 = 25.0 MGy).	INTRO
+57	78	electron-density maps	evidence	To avoid the previous necessity for visual inspection of electron-density maps to detect SRD sites, a computational approach was designed to quantify the electron-density change for each refined atom with increasing dose, thus providing a rapid systematic method for SRD study on such large multimeric complexes.	INTRO
+89	98	SRD sites	site	To avoid the previous necessity for visual inspection of electron-density maps to detect SRD sites, a computational approach was designed to quantify the electron-density change for each refined atom with increasing dose, thus providing a rapid systematic method for SRD study on such large multimeric complexes.	INTRO
+154	177	electron-density change	evidence	To avoid the previous necessity for visual inspection of electron-density maps to detect SRD sites, a computational approach was designed to quantify the electron-density change for each refined atom with increasing dose, thus providing a rapid systematic method for SRD study on such large multimeric complexes.	INTRO
+62	66	TRAP	complex_assembly	By employing the high 11-fold structural symmetry within each TRAP macromolecule, this approach permitted a thorough statistical quantification of the RD effects of RNA binding to TRAP.	INTRO
+165	168	RNA	chemical	By employing the high 11-fold structural symmetry within each TRAP macromolecule, this approach permitted a thorough statistical quantification of the RD effects of RNA binding to TRAP.	INTRO
+180	184	TRAP	complex_assembly	By employing the high 11-fold structural symmetry within each TRAP macromolecule, this approach permitted a thorough statistical quantification of the RD effects of RNA binding to TRAP.	INTRO
+0	43	Per-atom quantification of electron density	experimental_method	Per-atom quantification of electron density   	RESULTS
+175	198	electron-density change	evidence	To quantify the exact effects of nucleic acid binding to a protein on SRD susceptibility, a high-throughput and automated pipeline was created to systematically calculate the electron-density change for every refined atom within the TRAP–RNA structure as a function of dose.	RESULTS
+233	241	TRAP–RNA	complex_assembly	To quantify the exact effects of nucleic acid binding to a protein on SRD susceptibility, a high-throughput and automated pipeline was created to systematically calculate the electron-density change for every refined atom within the TRAP–RNA structure as a function of dose.	RESULTS
+242	251	structure	evidence	To quantify the exact effects of nucleic acid binding to a protein on SRD susceptibility, a high-throughput and automated pipeline was created to systematically calculate the electron-density change for every refined atom within the TRAP–RNA structure as a function of dose.	RESULTS
+49	70	density–dose dynamics	evidence	This provides an atom-specific quantification of density–dose dynamics, which was previously lacking within the field.	RESULTS
+36	45	SRD sites	site	Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible.	RESULTS
+73	125	F obs(d n) − F obs(d 1) Fourier difference map peaks	evidence	Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible.	RESULTS
+142	147	sigma	evidence	Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible.	RESULTS
+149	150	σ	evidence	Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible.	RESULTS
+181	200	standard deviations	evidence	Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible.	RESULTS
+210	241	mean map electron-density value	evidence	Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible.	RESULTS
+15	16	σ	evidence	However, these σ levels depend on the standard deviation values of the map, which can deviate between data sets, and are thus unsuitable for quantitative comparison of density between different dose data sets.	RESULTS
+38	56	standard deviation	evidence	However, these σ levels depend on the standard deviation values of the map, which can deviate between data sets, and are thus unsuitable for quantitative comparison of density between different dose data sets.	RESULTS
+71	74	map	evidence	However, these σ levels depend on the standard deviation values of the map, which can deviate between data sets, and are thus unsuitable for quantitative comparison of density between different dose data sets.	RESULTS
+168	175	density	evidence	However, these σ levels depend on the standard deviation values of the map, which can deviate between data sets, and are thus unsuitable for quantitative comparison of density between different dose data sets.	RESULTS
+23	50	maximum density-loss metric	evidence	Instead, we use here a maximum density-loss metric (D loss), which is the per-atom equivalent of the magnitude of these negative Fourier difference map peaks in units of e Å−3.	RESULTS
+52	58	D loss	evidence	Instead, we use here a maximum density-loss metric (D loss), which is the per-atom equivalent of the magnitude of these negative Fourier difference map peaks in units of e Å−3.	RESULTS
+120	157	negative Fourier difference map peaks	evidence	Instead, we use here a maximum density-loss metric (D loss), which is the per-atom equivalent of the magnitude of these negative Fourier difference map peaks in units of e Å−3.	RESULTS
+15	21	D loss	evidence	Large positive D loss values indicate radiation-induced atomic disordering reproducibly throughout the unit cells with respect to the initial low-dose data set.	RESULTS
+9	17	TRAP–RNA	complex_assembly	For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a).	RESULTS
+32	45	D loss metric	evidence	For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a).	RESULTS
+102	105	SRD	experimental_method	For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a).	RESULTS
+131	134	Glu	residue_name	For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a).	RESULTS
+139	142	Asp	residue_name	For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a).	RESULTS
+188	202	difference map	evidence	For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a).	RESULTS
+21	25	TRAP	complex_assembly	The main sequence of TRAP does not contain any Trp and Cys residues (and thus contains no disulfide bonds).	RESULTS
+47	50	Trp	residue_name	The main sequence of TRAP does not contain any Trp and Cys residues (and thus contains no disulfide bonds).	RESULTS
+55	58	Cys	residue_name	The main sequence of TRAP does not contain any Trp and Cys residues (and thus contains no disulfide bonds).	RESULTS
+14	17	Trp	chemical	The substrate Trp amino-acid ligands also exhibited disordering of the free terminal carboxyl groups at higher doses (Fig. 2 ▸ a); however, no clear Fourier difference peaks could be observed visually.	RESULTS
+149	173	Fourier difference peaks	evidence	The substrate Trp amino-acid ligands also exhibited disordering of the free terminal carboxyl groups at higher doses (Fig. 2 ▸ a); however, no clear Fourier difference peaks could be observed visually.	RESULTS
+46	49	Gly	residue_name	Even for radiation-insensitive residues (e.g. Gly) the average D loss increases with dose: this is the effect of global radiation damage, since as dose increases the electron density associated with each refined atom becomes weaker as the atomic occupancy decreases (Fig. 2 ▸ b).	RESULTS
+63	69	D loss	evidence	Even for radiation-insensitive residues (e.g. Gly) the average D loss increases with dose: this is the effect of global radiation damage, since as dose increases the electron density associated with each refined atom becomes weaker as the atomic occupancy decreases (Fig. 2 ▸ b).	RESULTS
+166	182	electron density	evidence	Even for radiation-insensitive residues (e.g. Gly) the average D loss increases with dose: this is the effect of global radiation damage, since as dose increases the electron density associated with each refined atom becomes weaker as the atomic occupancy decreases (Fig. 2 ▸ b).	RESULTS
+5	8	Glu	residue_name	Only Glu and Asp residues exhibit a rate of D loss increase that consistently exceeds the average decay (Fig. 2 ▸ b, dashed line) at each dose.	RESULTS
+13	16	Asp	residue_name	Only Glu and Asp residues exhibit a rate of D loss increase that consistently exceeds the average decay (Fig. 2 ▸ b, dashed line) at each dose.	RESULTS
+44	50	D loss	evidence	Only Glu and Asp residues exhibit a rate of D loss increase that consistently exceeds the average decay (Fig. 2 ▸ b, dashed line) at each dose.	RESULTS
+12	18	D loss	evidence	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+90	93	Glu	residue_name	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+108	111	Asp	residue_name	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+352	355	CO2	chemical	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+406	414	oxidized	protein_state	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+415	418	Glu	residue_name	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+444	447	Asp	residue_name	The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts.	RESULTS
+0	3	RNA	chemical	RNA is less susceptible to electron-density loss than protein within the TRAP–RNA complex   	RESULTS
+27	43	electron-density	evidence	RNA is less susceptible to electron-density loss than protein within the TRAP–RNA complex   	RESULTS
+73	81	TRAP–RNA	complex_assembly	RNA is less susceptible to electron-density loss than protein within the TRAP–RNA complex   	RESULTS
+0	20	Visual inspection of	experimental_method	Visual inspection of Fourier difference maps illustrated the clear lack of RNA electron-density degradation with increasing dose compared with the obvious protein damage manifestations (Figs. 3 ▸ b and 3 ▸ c).	RESULTS
+21	44	Fourier difference maps	evidence	Visual inspection of Fourier difference maps illustrated the clear lack of RNA electron-density degradation with increasing dose compared with the obvious protein damage manifestations (Figs. 3 ▸ b and 3 ▸ c).	RESULTS
+75	78	RNA	chemical	Visual inspection of Fourier difference maps illustrated the clear lack of RNA electron-density degradation with increasing dose compared with the obvious protein damage manifestations (Figs. 3 ▸ b and 3 ▸ c).	RESULTS
+79	107	electron-density degradation	evidence	Visual inspection of Fourier difference maps illustrated the clear lack of RNA electron-density degradation with increasing dose compared with the obvious protein damage manifestations (Figs. 3 ▸ b and 3 ▸ c).	RESULTS
+82	85	RNA	chemical	Only at the highest doses investigated (>20 MGy) was density loss observed at the RNA phosphate and C—O bonds of the phosphodiester backbone.	RESULTS
+20	26	D loss	evidence	However, the median D loss was lower by a factor of >2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3).	RESULTS
+59	62	RNA	chemical	However, the median D loss was lower by a factor of >2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3).	RESULTS
+80	83	Glu	residue_name	However, the median D loss was lower by a factor of >2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3).	RESULTS
+88	91	Asp	residue_name	However, the median D loss was lower by a factor of >2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3).	RESULTS
+207	210	Gly	residue_name	However, the median D loss was lower by a factor of >2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3).	RESULTS
+227	231	TRAP	complex_assembly	However, the median D loss was lower by a factor of >2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3).	RESULTS
+0	3	RNA	chemical	RNA binding protects radiation-sensitive residues   	RESULTS
+44	48	TRAP	complex_assembly	For the large number of acidic residues per TRAP ring (four Asp and six Glu residues per protein monomer), a strong dependence of decarboxylation susceptibility on local environment was observed (Fig. 4 ▸).	RESULTS
+49	53	ring	structure_element	For the large number of acidic residues per TRAP ring (four Asp and six Glu residues per protein monomer), a strong dependence of decarboxylation susceptibility on local environment was observed (Fig. 4 ▸).	RESULTS
+60	63	Asp	residue_name	For the large number of acidic residues per TRAP ring (four Asp and six Glu residues per protein monomer), a strong dependence of decarboxylation susceptibility on local environment was observed (Fig. 4 ▸).	RESULTS
+72	75	Glu	residue_name	For the large number of acidic residues per TRAP ring (four Asp and six Glu residues per protein monomer), a strong dependence of decarboxylation susceptibility on local environment was observed (Fig. 4 ▸).	RESULTS
+97	104	monomer	oligomeric_state	For the large number of acidic residues per TRAP ring (four Asp and six Glu residues per protein monomer), a strong dependence of decarboxylation susceptibility on local environment was observed (Fig. 4 ▸).	RESULTS
+9	12	Glu	residue_name	For each Glu Cδ or Asp Cγ atom, D loss provided a direct measure of the rate of side-chain carboxyl-group disordering and subsequent decarboxylation.	RESULTS
+19	22	Asp	residue_name	For each Glu Cδ or Asp Cγ atom, D loss provided a direct measure of the rate of side-chain carboxyl-group disordering and subsequent decarboxylation.	RESULTS
+32	38	D loss	evidence	For each Glu Cδ or Asp Cγ atom, D loss provided a direct measure of the rate of side-chain carboxyl-group disordering and subsequent decarboxylation.	RESULTS
+59	67	nonbound	protein_state	For acidic residues with no differing interactions between nonbound and bound TRAP (Fig. 4 ▸ a), similar damage was apparent between the two rings within the asymmetric unit, as expected.	RESULTS
+72	77	bound	protein_state	For acidic residues with no differing interactions between nonbound and bound TRAP (Fig. 4 ▸ a), similar damage was apparent between the two rings within the asymmetric unit, as expected.	RESULTS
+78	82	TRAP	complex_assembly	For acidic residues with no differing interactions between nonbound and bound TRAP (Fig. 4 ▸ a), similar damage was apparent between the two rings within the asymmetric unit, as expected.	RESULTS
+9	13	TRAP	complex_assembly	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+39	61	RNA-binding interfaces	site	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+103	111	nonbound	protein_state	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+112	116	TRAP	complex_assembly	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+155	175	ring–ring interfaces	site	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+215	220	bound	protein_state	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+221	225	TRAP	complex_assembly	However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c).	RESULTS
+23	28	Glu36	residue_name_number	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+30	35	Asp39	residue_name_number	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+40	45	Glu42	residue_name_number	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+63	66	RNA	chemical	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+102	106	TRAP	complex_assembly	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+107	111	ring	structure_element	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+112	120	subunits	structure_element	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+147	162	density changes	evidence	Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose.	RESULTS
+0	26	Hotelling’s T-squared test	experimental_method	Hotelling’s T-squared test (the multivariate counterpart of Student’s t-test) was used to reject the null hypothesis that the means of the D loss metric were equal for the bound and nonbound groups in Fig. 5 ▸.	RESULTS
+60	76	Student’s t-test	experimental_method	Hotelling’s T-squared test (the multivariate counterpart of Student’s t-test) was used to reject the null hypothesis that the means of the D loss metric were equal for the bound and nonbound groups in Fig. 5 ▸.	RESULTS
+139	152	D loss metric	evidence	Hotelling’s T-squared test (the multivariate counterpart of Student’s t-test) was used to reject the null hypothesis that the means of the D loss metric were equal for the bound and nonbound groups in Fig. 5 ▸.	RESULTS
+172	177	bound	protein_state	Hotelling’s T-squared test (the multivariate counterpart of Student’s t-test) was used to reject the null hypothesis that the means of the D loss metric were equal for the bound and nonbound groups in Fig. 5 ▸.	RESULTS
+182	190	nonbound	protein_state	Hotelling’s T-squared test (the multivariate counterpart of Student’s t-test) was used to reject the null hypothesis that the means of the D loss metric were equal for the bound and nonbound groups in Fig. 5 ▸.	RESULTS
+27	33	D loss	evidence	A significant reduction in D loss is seen for Glu36 in RNA-bound compared with nonbound TRAP, indicative of a lower rate of side-chain decarboxylation (Fig. 5 ▸ a; p = 6.06 × 10−5).	RESULTS
+46	51	Glu36	residue_name_number	A significant reduction in D loss is seen for Glu36 in RNA-bound compared with nonbound TRAP, indicative of a lower rate of side-chain decarboxylation (Fig. 5 ▸ a; p = 6.06 × 10−5).	RESULTS
+55	64	RNA-bound	protein_state	A significant reduction in D loss is seen for Glu36 in RNA-bound compared with nonbound TRAP, indicative of a lower rate of side-chain decarboxylation (Fig. 5 ▸ a; p = 6.06 × 10−5).	RESULTS
+79	87	nonbound	protein_state	A significant reduction in D loss is seen for Glu36 in RNA-bound compared with nonbound TRAP, indicative of a lower rate of side-chain decarboxylation (Fig. 5 ▸ a; p = 6.06 × 10−5).	RESULTS
+88	92	TRAP	complex_assembly	A significant reduction in D loss is seen for Glu36 in RNA-bound compared with nonbound TRAP, indicative of a lower rate of side-chain decarboxylation (Fig. 5 ▸ a; p = 6.06 × 10−5).	RESULTS
+9	13	TRAP	complex_assembly	For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base.	RESULTS
+14	18	ring	structure_element	For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base.	RESULTS
+19	26	subunit	structure_element	For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base.	RESULTS
+32	37	Glu36	residue_name_number	For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base.	RESULTS
+125	127	G3	residue_name_number	For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base.	RESULTS
+128	131	RNA	chemical	For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base.	RESULTS
+17	22	Asp39	residue_name_number	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+30	47	TRAP–(GAGUU)10GAG	complex_assembly	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+48	57	structure	evidence	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+112	114	G1	residue_name_number	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+142	161	TRAP–RNA interfaces	site	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+171	176	Glu36	residue_name_number	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+180	182	G3	residue_name_number	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+210	217	density	evidence	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+235	238	RNA	chemical	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+275	280	Asp39	residue_name_number	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+290	295	Glu36	residue_name_number	In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925).	RESULTS
+0	3	RNA	chemical	RNA binding reduces radiation-induced disorder on the atomic scale   	RESULTS
+20	25	Glu42	residue_name_number	One oxygen (O∊1) of Glu42 appears to form a hydrogen bond to a nearby water within each TRAP RNA-binding pocket, with the other (O∊2) being involved in a salt-bridge interaction with Arg58 (Hopcroft et al., 2002; Antson et al., 1999).	RESULTS
+70	75	water	chemical	One oxygen (O∊1) of Glu42 appears to form a hydrogen bond to a nearby water within each TRAP RNA-binding pocket, with the other (O∊2) being involved in a salt-bridge interaction with Arg58 (Hopcroft et al., 2002; Antson et al., 1999).	RESULTS
+88	111	TRAP RNA-binding pocket	site	One oxygen (O∊1) of Glu42 appears to form a hydrogen bond to a nearby water within each TRAP RNA-binding pocket, with the other (O∊2) being involved in a salt-bridge interaction with Arg58 (Hopcroft et al., 2002; Antson et al., 1999).	RESULTS
+183	188	Arg58	residue_name_number	One oxygen (O∊1) of Glu42 appears to form a hydrogen bond to a nearby water within each TRAP RNA-binding pocket, with the other (O∊2) being involved in a salt-bridge interaction with Arg58 (Hopcroft et al., 2002; Antson et al., 1999).	RESULTS
+70	79	glutamate	residue_name	Salt-bridge interactions have previously been suggested to reduce the glutamate decarboxylation rate within the large (∼62.4 kDa) myrosinase protein structure (Burmeister, 2000).	RESULTS
+130	140	myrosinase	protein_type	Salt-bridge interactions have previously been suggested to reduce the glutamate decarboxylation rate within the large (∼62.4 kDa) myrosinase protein structure (Burmeister, 2000).	RESULTS
+149	158	structure	evidence	Salt-bridge interactions have previously been suggested to reduce the glutamate decarboxylation rate within the large (∼62.4 kDa) myrosinase protein structure (Burmeister, 2000).	RESULTS
+50	65	D loss dynamics	evidence	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+74	82	nonbound	protein_state	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+83	88	bound	protein_state	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+89	94	Glu42	residue_name_number	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+145	150	Glu42	residue_name_number	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+278	281	RNA	chemical	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+303	308	water	chemical	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+399	409	absence of	protein_state	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+410	413	RNA	chemical	A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA.	RESULTS
+4	27	density-change dynamics	evidence	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+73	78	bound	protein_state	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+83	91	nonbound	protein_state	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+92	96	TRAP	complex_assembly	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+106	111	Glu42	residue_name_number	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+169	172	RNA	chemical	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+251	256	Glu42	residue_name_number	The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate.	RESULTS
+4	7	RNA	chemical	The RNA-stabilizing effect was not restricted to radiation-sensitive acidic residues.	RESULTS
+18	23	Phe32	residue_name_number	The side chain of Phe32 stacks against the G3 base within the 11 TRAP RNA-binding interfaces (Antson et al., 1999).	RESULTS
+43	45	G3	residue_name_number	The side chain of Phe32 stacks against the G3 base within the 11 TRAP RNA-binding interfaces (Antson et al., 1999).	RESULTS
+65	92	TRAP RNA-binding interfaces	site	The side chain of Phe32 stacks against the G3 base within the 11 TRAP RNA-binding interfaces (Antson et al., 1999).	RESULTS
+26	32	D loss	evidence	With increasing dose, the D loss associated with the Phe32 side chain was significantly reduced upon RNA binding (Fig. 5 ▸ e; Phe32 Cζ; p = 0.0014), an indication that radiation-induced conformation disordering of Phe32 had been reduced.	RESULTS
+53	58	Phe32	residue_name_number	With increasing dose, the D loss associated with the Phe32 side chain was significantly reduced upon RNA binding (Fig. 5 ▸ e; Phe32 Cζ; p = 0.0014), an indication that radiation-induced conformation disordering of Phe32 had been reduced.	RESULTS
+101	104	RNA	chemical	With increasing dose, the D loss associated with the Phe32 side chain was significantly reduced upon RNA binding (Fig. 5 ▸ e; Phe32 Cζ; p = 0.0014), an indication that radiation-induced conformation disordering of Phe32 had been reduced.	RESULTS
+126	131	Phe32	residue_name_number	With increasing dose, the D loss associated with the Phe32 side chain was significantly reduced upon RNA binding (Fig. 5 ▸ e; Phe32 Cζ; p = 0.0014), an indication that radiation-induced conformation disordering of Phe32 had been reduced.	RESULTS
+214	219	Phe32	residue_name_number	With increasing dose, the D loss associated with the Phe32 side chain was significantly reduced upon RNA binding (Fig. 5 ▸ e; Phe32 Cζ; p = 0.0014), an indication that radiation-induced conformation disordering of Phe32 had been reduced.	RESULTS
+23	28	Lys37	residue_name_number	The extended aliphatic Lys37 side chain stacks against the nearby G1 base, making a series of nonpolar contacts within each RNA-binding interface.	RESULTS
+66	68	G1	residue_name_number	The extended aliphatic Lys37 side chain stacks against the nearby G1 base, making a series of nonpolar contacts within each RNA-binding interface.	RESULTS
+124	145	RNA-binding interface	site	The extended aliphatic Lys37 side chain stacks against the nearby G1 base, making a series of nonpolar contacts within each RNA-binding interface.	RESULTS
+4	10	D loss	evidence	The D loss for Lys37 side-chain atoms was also reduced when stacked against the G1 base (Fig. 5 ▸ f; p = 0.0243 for Lys37 C∊ atoms).	RESULTS
+15	20	Lys37	residue_name_number	The D loss for Lys37 side-chain atoms was also reduced when stacked against the G1 base (Fig. 5 ▸ f; p = 0.0243 for Lys37 C∊ atoms).	RESULTS
+80	82	G1	residue_name_number	The D loss for Lys37 side-chain atoms was also reduced when stacked against the G1 base (Fig. 5 ▸ f; p = 0.0243 for Lys37 C∊ atoms).	RESULTS
+116	121	Lys37	residue_name_number	The D loss for Lys37 side-chain atoms was also reduced when stacked against the G1 base (Fig. 5 ▸ f; p = 0.0243 for Lys37 C∊ atoms).	RESULTS
+15	20	Phe32	residue_name_number	Representative Phe32 and Lys37 atoms were selected to illustrate these trends.	RESULTS
+25	30	Lys37	residue_name_number	Representative Phe32 and Lys37 atoms were selected to illustrate these trends.	RESULTS
+6	8	MX	experimental_method	Here, MX radiation-induced specific structural changes within the large TRAP–RNA assembly over a large dose range (1.3–25.0 MGy) have been analysed using a high-throughput quantitative approach, providing a measure of the electron-density distribution for each refined atom with increasing dose, D loss.	DISCUSS
+72	80	TRAP–RNA	complex_assembly	Here, MX radiation-induced specific structural changes within the large TRAP–RNA assembly over a large dose range (1.3–25.0 MGy) have been analysed using a high-throughput quantitative approach, providing a measure of the electron-density distribution for each refined atom with increasing dose, D loss.	DISCUSS
+222	251	electron-density distribution	evidence	Here, MX radiation-induced specific structural changes within the large TRAP–RNA assembly over a large dose range (1.3–25.0 MGy) have been analysed using a high-throughput quantitative approach, providing a measure of the electron-density distribution for each refined atom with increasing dose, D loss.	DISCUSS
+296	302	D loss	evidence	Here, MX radiation-induced specific structural changes within the large TRAP–RNA assembly over a large dose range (1.3–25.0 MGy) have been analysed using a high-throughput quantitative approach, providing a measure of the electron-density distribution for each refined atom with increasing dose, D loss.	DISCUSS
+118	120	MX	experimental_method	Compared with previous studies, the results provide a further step in the detailed characterization of SRD effects in MX.	DISCUSS
+173	225	F obs(d n) − F obs(d 1) Fourier difference map peaks	evidence	Our method­ology, which eliminated tedious and error-prone visual inspection, permitted the determination on a per-atom basis of the most damaged sites, as characterized by F obs(d n) − F obs(d 1) Fourier difference map peaks between successive data sets collected from the same crystal.	DISCUSS
+279	286	crystal	evidence	Our method­ology, which eliminated tedious and error-prone visual inspection, permitted the determination on a per-atom basis of the most damaged sites, as characterized by F obs(d n) − F obs(d 1) Fourier difference map peaks between successive data sets collected from the same crystal.	DISCUSS
+65	68	RNA	chemical	Here, it provided the precision required to quantify the role of RNA in the damage susceptibilities of equivalent atoms between RNA-bound and nonbound TRAP, but it is applicable to any MX SRD study.	DISCUSS
+128	137	RNA-bound	protein_state	Here, it provided the precision required to quantify the role of RNA in the damage susceptibilities of equivalent atoms between RNA-bound and nonbound TRAP, but it is applicable to any MX SRD study.	DISCUSS
+142	150	nonbound	protein_state	Here, it provided the precision required to quantify the role of RNA in the damage susceptibilities of equivalent atoms between RNA-bound and nonbound TRAP, but it is applicable to any MX SRD study.	DISCUSS
+151	155	TRAP	complex_assembly	Here, it provided the precision required to quantify the role of RNA in the damage susceptibilities of equivalent atoms between RNA-bound and nonbound TRAP, but it is applicable to any MX SRD study.	DISCUSS
+185	187	MX	experimental_method	Here, it provided the precision required to quantify the role of RNA in the damage susceptibilities of equivalent atoms between RNA-bound and nonbound TRAP, but it is applicable to any MX SRD study.	DISCUSS
+4	7	RNA	chemical	The RNA was found to be substantially more radiation-resistant than the protein, even at the highest doses investigated (∼25.0 MGy), which is in strong concurrence with our previous SRD investigation of the C.Esp1396I protein–DNA complex (Bury et al., 2015).	DISCUSS
+43	62	radiation-resistant	protein_state	The RNA was found to be substantially more radiation-resistant than the protein, even at the highest doses investigated (∼25.0 MGy), which is in strong concurrence with our previous SRD investigation of the C.Esp1396I protein–DNA complex (Bury et al., 2015).	DISCUSS
+182	199	SRD investigation	experimental_method	The RNA was found to be substantially more radiation-resistant than the protein, even at the highest doses investigated (∼25.0 MGy), which is in strong concurrence with our previous SRD investigation of the C.Esp1396I protein–DNA complex (Bury et al., 2015).	DISCUSS
+207	217	C.Esp1396I	complex_assembly	The RNA was found to be substantially more radiation-resistant than the protein, even at the highest doses investigated (∼25.0 MGy), which is in strong concurrence with our previous SRD investigation of the C.Esp1396I protein–DNA complex (Bury et al., 2015).	DISCUSS
+226	229	DNA	chemical	The RNA was found to be substantially more radiation-resistant than the protein, even at the highest doses investigated (∼25.0 MGy), which is in strong concurrence with our previous SRD investigation of the C.Esp1396I protein–DNA complex (Bury et al., 2015).	DISCUSS
+60	95	F obs(d n) − F obs(d 1) map density	evidence	Consistent with that study, at high doses of above ∼20 MGy, F obs(d n) − F obs(d 1) map density was detected around P, O3′ and O5′ atoms of the RNA backbone, with no significant difference density localized to RNA ribose and basic subunits.	DISCUSS
+144	147	RNA	chemical	Consistent with that study, at high doses of above ∼20 MGy, F obs(d n) − F obs(d 1) map density was detected around P, O3′ and O5′ atoms of the RNA backbone, with no significant difference density localized to RNA ribose and basic subunits.	DISCUSS
+178	196	difference density	evidence	Consistent with that study, at high doses of above ∼20 MGy, F obs(d n) − F obs(d 1) map density was detected around P, O3′ and O5′ atoms of the RNA backbone, with no significant difference density localized to RNA ribose and basic subunits.	DISCUSS
+210	213	RNA	chemical	Consistent with that study, at high doses of above ∼20 MGy, F obs(d n) − F obs(d 1) map density was detected around P, O3′ and O5′ atoms of the RNA backbone, with no significant difference density localized to RNA ribose and basic subunits.	DISCUSS
+231	239	subunits	structure_element	Consistent with that study, at high doses of above ∼20 MGy, F obs(d n) − F obs(d 1) map density was detected around P, O3′ and O5′ atoms of the RNA backbone, with no significant difference density localized to RNA ribose and basic subunits.	DISCUSS
+0	3	RNA	chemical	RNA backbone disordering thus appears to be the main radiation-induced effect in RNA, with the protein–base interactions maintained even at high doses (>20 MGy).	DISCUSS
+81	84	RNA	chemical	RNA backbone disordering thus appears to be the main radiation-induced effect in RNA, with the protein–base interactions maintained even at high doses (>20 MGy).	DISCUSS
+4	6	U4	residue_name_number	The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4).	DISCUSS
+7	16	phosphate	chemical	The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4).	DISCUSS
+45	51	D loss	evidence	The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4).	DISCUSS
+77	79	G1	residue_name_number	The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4).	DISCUSS
+81	83	A2	residue_name_number	The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4).	DISCUSS
+88	90	G3	residue_name_number	The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4).	DISCUSS
+6	8	U4	residue_name_number	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+100	104	TRAP	complex_assembly	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+113	118	water	chemical	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+175	183	subunits	structure_element	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+197	202	Arg58	residue_name_number	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+245	253	subunits	structure_element	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+271	273	U4	residue_name_number	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+274	280	D loss	evidence	Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility.	DISCUSS
+34	37	RNA	chemical	At 25.0 MGy, the magnitude of the RNA backbone D loss was of the same order as for the radiation-insensitive Gly Cα atoms and on average less than half that of the acidic residues of the protein (Supplementary Fig. S3).	DISCUSS
+47	53	D loss	evidence	At 25.0 MGy, the magnitude of the RNA backbone D loss was of the same order as for the radiation-insensitive Gly Cα atoms and on average less than half that of the acidic residues of the protein (Supplementary Fig. S3).	DISCUSS
+109	112	Gly	residue_name	At 25.0 MGy, the magnitude of the RNA backbone D loss was of the same order as for the radiation-insensitive Gly Cα atoms and on average less than half that of the acidic residues of the protein (Supplementary Fig. S3).	DISCUSS
+72	75	RNA	chemical	Consequently, no clear single-strand breaks could be located, and since RNA-binding within the current TRAP–(GAGUU)10GAG complex is mediated predominantly through base–protein interactions, the biological integrity of the RNA complex was dictated by the rate at which protein decarboxylation occurred.	DISCUSS
+103	120	TRAP–(GAGUU)10GAG	complex_assembly	Consequently, no clear single-strand breaks could be located, and since RNA-binding within the current TRAP–(GAGUU)10GAG complex is mediated predominantly through base–protein interactions, the biological integrity of the RNA complex was dictated by the rate at which protein decarboxylation occurred.	DISCUSS
+222	225	RNA	chemical	Consequently, no clear single-strand breaks could be located, and since RNA-binding within the current TRAP–(GAGUU)10GAG complex is mediated predominantly through base–protein interactions, the biological integrity of the RNA complex was dictated by the rate at which protein decarboxylation occurred.	DISCUSS
+0	3	RNA	chemical	RNA interacting with TRAP was shown to offer significant protection against radiation-induced structural changes.	DISCUSS
+21	25	TRAP	complex_assembly	RNA interacting with TRAP was shown to offer significant protection against radiation-induced structural changes.	DISCUSS
+5	10	Glu36	residue_name_number	Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively).	DISCUSS
+15	20	Asp39	residue_name_number	Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively).	DISCUSS
+38	41	RNA	chemical	Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively).	DISCUSS
+78	85	guanine	chemical	Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively).	DISCUSS
+93	95	G3	residue_name_number	Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively).	DISCUSS
+100	102	G1	residue_name_number	Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively).	DISCUSS
+23	28	Asp39	residue_name_number	However, compared with Asp39, Glu36 is strikingly less decarboxylated when bound to RNA (Fig. 4 ▸).	DISCUSS
+30	35	Glu36	residue_name_number	However, compared with Asp39, Glu36 is strikingly less decarboxylated when bound to RNA (Fig. 4 ▸).	DISCUSS
+75	83	bound to	protein_state	However, compared with Asp39, Glu36 is strikingly less decarboxylated when bound to RNA (Fig. 4 ▸).	DISCUSS
+84	87	RNA	chemical	However, compared with Asp39, Glu36 is strikingly less decarboxylated when bound to RNA (Fig. 4 ▸).	DISCUSS
+40	83	mutagenesis and nucleoside analogue studies	experimental_method	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+133	135	G1	residue_name_number	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+164	168	TRAP	complex_assembly	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+187	189	A2	residue_name_number	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+194	196	G3	residue_name_number	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+232	252	RNA-binding affinity	evidence	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+256	260	TRAP	complex_assembly	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+262	265	K d	evidence	This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM).	DISCUSS
+4	9	Glu36	residue_name_number	For Glu36 and Asp39, no direct quantitative correlation could be established between hydrogen-bond length and D loss (linear R 2 of <0.23 for all doses; Supplementary Fig. S5).	DISCUSS
+14	19	Asp39	residue_name_number	For Glu36 and Asp39, no direct quantitative correlation could be established between hydrogen-bond length and D loss (linear R 2 of <0.23 for all doses; Supplementary Fig. S5).	DISCUSS
+110	116	D loss	evidence	For Glu36 and Asp39, no direct quantitative correlation could be established between hydrogen-bond length and D loss (linear R 2 of <0.23 for all doses; Supplementary Fig. S5).	DISCUSS
+118	128	linear R 2	evidence	For Glu36 and Asp39, no direct quantitative correlation could be established between hydrogen-bond length and D loss (linear R 2 of <0.23 for all doses; Supplementary Fig. S5).	DISCUSS
+69	74	Glu36	residue_name_number	Thus, another factor must be responsible for this clear reduction in Glu36 CO2 decarboxyl­ation in RNA-bound TRAP.	DISCUSS
+99	108	RNA-bound	protein_state	Thus, another factor must be responsible for this clear reduction in Glu36 CO2 decarboxyl­ation in RNA-bound TRAP.	DISCUSS
+109	113	TRAP	complex_assembly	Thus, another factor must be responsible for this clear reduction in Glu36 CO2 decarboxyl­ation in RNA-bound TRAP.	DISCUSS
+4	9	Glu36	residue_name_number	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+71	76	His34	residue_name_number	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+81	86	Lys56	residue_name_number	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+121	130	conserved	protein_state	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+147	149	G3	residue_name_number	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+231	236	Glu36	residue_name_number	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+240	249	RNA-bound	protein_state	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+250	254	TRAP	complex_assembly	The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP.	DISCUSS
+5	13	bound to	protein_state	When bound to RNA, the average solvent-accessible area of the Glu36 side-chain O atoms is reduced from ∼15 to 0 Å2.	DISCUSS
+14	17	RNA	chemical	When bound to RNA, the average solvent-accessible area of the Glu36 side-chain O atoms is reduced from ∼15 to 0 Å2.	DISCUSS
+62	67	Glu36	residue_name_number	When bound to RNA, the average solvent-accessible area of the Glu36 side-chain O atoms is reduced from ∼15 to 0 Å2.	DISCUSS
+46	51	Glu36	residue_name_number	We propose that with no solvent accessibility Glu36 decarboxylation is inhibited, since the CO2-formation rate K 2 is greatly reduced, and suggest that steric hindrance prevents each radicalized Glu36 CO2 group from achieving the planar conformation required for complete dissociation from TRAP.	DISCUSS
+92	114	CO2-formation rate K 2	evidence	We propose that with no solvent accessibility Glu36 decarboxylation is inhibited, since the CO2-formation rate K 2 is greatly reduced, and suggest that steric hindrance prevents each radicalized Glu36 CO2 group from achieving the planar conformation required for complete dissociation from TRAP.	DISCUSS
+195	200	Glu36	residue_name_number	We propose that with no solvent accessibility Glu36 decarboxylation is inhibited, since the CO2-formation rate K 2 is greatly reduced, and suggest that steric hindrance prevents each radicalized Glu36 CO2 group from achieving the planar conformation required for complete dissociation from TRAP.	DISCUSS
+290	294	TRAP	complex_assembly	We propose that with no solvent accessibility Glu36 decarboxylation is inhibited, since the CO2-formation rate K 2 is greatly reduced, and suggest that steric hindrance prevents each radicalized Glu36 CO2 group from achieving the planar conformation required for complete dissociation from TRAP.	DISCUSS
+4	36	electron-recombination rate K −1	evidence	The electron-recombination rate K −1 remains high, however, owing to rapid electron migration through the protein–RNA complex to refill the Glu36 positive hole (the precursor for Glu decarboxylation).	DISCUSS
+106	117	protein–RNA	complex_assembly	The electron-recombination rate K −1 remains high, however, owing to rapid electron migration through the protein–RNA complex to refill the Glu36 positive hole (the precursor for Glu decarboxylation).	DISCUSS
+140	145	Glu36	residue_name_number	The electron-recombination rate K −1 remains high, however, owing to rapid electron migration through the protein–RNA complex to refill the Glu36 positive hole (the precursor for Glu decarboxylation).	DISCUSS
+146	159	positive hole	site	The electron-recombination rate K −1 remains high, however, owing to rapid electron migration through the protein–RNA complex to refill the Glu36 positive hole (the precursor for Glu decarboxylation).	DISCUSS
+179	182	Glu	residue_name	The electron-recombination rate K −1 remains high, however, owing to rapid electron migration through the protein–RNA complex to refill the Glu36 positive hole (the precursor for Glu decarboxylation).	DISCUSS
+5	8	RNA	chemical	Upon RNA binding, the Asp39 side-chain carboxyl group solvent-accessible area changes from ∼75 to 35 Å2, still allowing a high CO2-formation rate K 2.	DISCUSS
+22	27	Asp39	residue_name_number	Upon RNA binding, the Asp39 side-chain carboxyl group solvent-accessible area changes from ∼75 to 35 Å2, still allowing a high CO2-formation rate K 2.	DISCUSS
+127	130	CO2	chemical	Upon RNA binding, the Asp39 side-chain carboxyl group solvent-accessible area changes from ∼75 to 35 Å2, still allowing a high CO2-formation rate K 2.	DISCUSS
+141	149	rate K 2	evidence	Upon RNA binding, the Asp39 side-chain carboxyl group solvent-accessible area changes from ∼75 to 35 Å2, still allowing a high CO2-formation rate K 2.	DISCUSS
+86	93	crystal	evidence	The prevalence of radical attack from solvent channels surrounding the protein in the crystal is a questionable cause, considering previous observations indicating that the strongly oxidizing hydroxyl radical is immobile at 100 K (Allan et al., 2013; Owen et al., 2012).	DISCUSS
+40	44	with	protein_state	By comparing equivalent acidic residues with and without RNA, we have now deconvoluted the role of solvent accessibility from other local protein environment factors, and thus propose a suitable mechanism by which exceptionally low solvent accessibility can reduce the rate of decarboxylation.	DISCUSS
+49	56	without	protein_state	By comparing equivalent acidic residues with and without RNA, we have now deconvoluted the role of solvent accessibility from other local protein environment factors, and thus propose a suitable mechanism by which exceptionally low solvent accessibility can reduce the rate of decarboxylation.	DISCUSS
+57	60	RNA	chemical	By comparing equivalent acidic residues with and without RNA, we have now deconvoluted the role of solvent accessibility from other local protein environment factors, and thus propose a suitable mechanism by which exceptionally low solvent accessibility can reduce the rate of decarboxylation.	DISCUSS
+17	39	RNA-binding interfaces	site	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+41	44	RNA	chemical	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+102	107	Glu50	residue_name_number	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+109	114	Glu71	residue_name_number	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+119	124	Glu73	residue_name_number	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+180	184	TRAP	complex_assembly	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+185	190	rings	structure_element	Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c).	DISCUSS
+89	94	bound	protein_state	However, for each of these residues the exact crystal contacts are not preserved between bound and nonbound TRAP or even between monomers within one TRAP ring.	DISCUSS
+99	107	nonbound	protein_state	However, for each of these residues the exact crystal contacts are not preserved between bound and nonbound TRAP or even between monomers within one TRAP ring.	DISCUSS
+108	112	TRAP	complex_assembly	However, for each of these residues the exact crystal contacts are not preserved between bound and nonbound TRAP or even between monomers within one TRAP ring.	DISCUSS
+149	153	TRAP	complex_assembly	However, for each of these residues the exact crystal contacts are not preserved between bound and nonbound TRAP or even between monomers within one TRAP ring.	DISCUSS
+154	158	ring	structure_element	However, for each of these residues the exact crystal contacts are not preserved between bound and nonbound TRAP or even between monomers within one TRAP ring.	DISCUSS
+16	21	bound	protein_state	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+22	26	TRAP	complex_assembly	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+28	33	Glu73	residue_name_number	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+61	67	lysine	residue_name	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+86	94	subunits	structure_element	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+107	115	nonbound	protein_state	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+116	120	TRAP	complex_assembly	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+152	157	Glu73	residue_name_number	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+202	208	waters	chemical	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+217	224	subunit	structure_element	For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit.	DISCUSS
+95	113	SRD investigations	experimental_method	Radiation-induced side-chain conformational changes have been poorly characterized in previous SRD investigations owing to their strong dependence on packing density and geometric strain.	DISCUSS
+205	207	MX	experimental_method	Such structural changes are known to have significant roles within enzymatic pathways, and experimenters must be aware of these possible confounding factors when assigning true functional mechanisms using MX.	DISCUSS
+22	25	RNA	chemical	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+37	41	TRAP	complex_assembly	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+95	99	TRAP	complex_assembly	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+128	133	Lys37	residue_name_number	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+138	143	Phe32	residue_name_number	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+169	171	G1	residue_name_number	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+176	178	G3	residue_name_number	Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively.	DISCUSS
+46	49	Tyr	residue_name	It has been suggested (Burmeister, 2000) that Tyr residues can lose their aromatic –OH group owing to radiation-induced effects; however, no energetically favourable pathway for –OH cleavage exists and this has not been detected in aqueous radiation-chemistry studies.	DISCUSS
+3	7	TRAP	complex_assembly	In TRAP, D loss increased at a similar rate for both the Tyr O atoms and aromatic ring atoms, suggesting that full ring conformational disordering is more likely.	DISCUSS
+9	15	D loss	evidence	In TRAP, D loss increased at a similar rate for both the Tyr O atoms and aromatic ring atoms, suggesting that full ring conformational disordering is more likely.	DISCUSS
+57	60	Tyr	residue_name	In TRAP, D loss increased at a similar rate for both the Tyr O atoms and aromatic ring atoms, suggesting that full ring conformational disordering is more likely.	DISCUSS
+82	86	ring	structure_element	In TRAP, D loss increased at a similar rate for both the Tyr O atoms and aromatic ring atoms, suggesting that full ring conformational disordering is more likely.	DISCUSS
+115	119	ring	structure_element	In TRAP, D loss increased at a similar rate for both the Tyr O atoms and aromatic ring atoms, suggesting that full ring conformational disordering is more likely.	DISCUSS
+35	59	Fourier difference peaks	evidence	Indeed, no convincing reproducible Fourier difference peaks above the background map noise were observed around any Tyr terminal –OH groups.	DISCUSS
+81	84	map	evidence	Indeed, no convincing reproducible Fourier difference peaks above the background map noise were observed around any Tyr terminal –OH groups.	DISCUSS
+116	119	Tyr	residue_name	Indeed, no convincing reproducible Fourier difference peaks above the background map noise were observed around any Tyr terminal –OH groups.	DISCUSS
+4	7	RNA	chemical	The RNA-stabilization effects on protein are observed at short ranges and are restricted to within the RNA-binding interfaces around the TRAP ring.	DISCUSS
+103	125	RNA-binding interfaces	site	The RNA-stabilization effects on protein are observed at short ranges and are restricted to within the RNA-binding interfaces around the TRAP ring.	DISCUSS
+137	141	TRAP	complex_assembly	The RNA-stabilization effects on protein are observed at short ranges and are restricted to within the RNA-binding interfaces around the TRAP ring.	DISCUSS
+142	146	ring	structure_element	The RNA-stabilization effects on protein are observed at short ranges and are restricted to within the RNA-binding interfaces around the TRAP ring.	DISCUSS
+13	18	Asp17	residue_name_number	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+46	48	G1	residue_name_number	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+67	89	RNA-binding interfaces	site	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+127	145	loss dose-dynamics	evidence	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+154	163	RNA-bound	protein_state	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+168	176	nonbound	protein_state	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+177	181	TRAP	complex_assembly	For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p > 0.9).	DISCUSS
+214	225	DNA–protein	complex_assembly	An increase in the dose at which functionally important residues remain intact has biological ramifications for understanding the mechanisms at which ionizing radiation damage is mitigated within naturally forming DNA–protein and RNA–protein complexes.	DISCUSS
+230	241	RNA–protein	complex_assembly	An increase in the dose at which functionally important residues remain intact has biological ramifications for understanding the mechanisms at which ionizing radiation damage is mitigated within naturally forming DNA–protein and RNA–protein complexes.	DISCUSS
+55	64	DNA-bound	protein_state	Observations of lower protein radiation-sensitivity in DNA-bound forms have been recorded in solution at RT at much lower doses (∼1 kGy) than those used for typical MX experiments [e.g. an oestrogen response element–receptor complex (Stísová et al., 2006) and a DNA glycosylase and its abasic DNA target site (Gillard et al., 2004)].	DISCUSS
+165	167	MX	experimental_method	Observations of lower protein radiation-sensitivity in DNA-bound forms have been recorded in solution at RT at much lower doses (∼1 kGy) than those used for typical MX experiments [e.g. an oestrogen response element–receptor complex (Stísová et al., 2006) and a DNA glycosylase and its abasic DNA target site (Gillard et al., 2004)].	DISCUSS
+262	277	DNA glycosylase	protein_type	Observations of lower protein radiation-sensitivity in DNA-bound forms have been recorded in solution at RT at much lower doses (∼1 kGy) than those used for typical MX experiments [e.g. an oestrogen response element–receptor complex (Stísová et al., 2006) and a DNA glycosylase and its abasic DNA target site (Gillard et al., 2004)].	DISCUSS
+286	308	abasic DNA target site	site	Observations of lower protein radiation-sensitivity in DNA-bound forms have been recorded in solution at RT at much lower doses (∼1 kGy) than those used for typical MX experiments [e.g. an oestrogen response element–receptor complex (Stísová et al., 2006) and a DNA glycosylase and its abasic DNA target site (Gillard et al., 2004)].	DISCUSS
+191	194	DNA	chemical	In these studies, the main damaging species is predicted to be the oxidizing hydroxyl radical produced through solvent irradiation, which is known to add to double covalent bonds within both DNA and RNA bases to induce strand breaks and base modification (Spotheim-Maurizot & Davídková, 2011; Chance et al., 1997).	DISCUSS
+199	202	RNA	chemical	In these studies, the main damaging species is predicted to be the oxidizing hydroxyl radical produced through solvent irradiation, which is known to add to double covalent bonds within both DNA and RNA bases to induce strand breaks and base modification (Spotheim-Maurizot & Davídková, 2011; Chance et al., 1997).	DISCUSS
+44	47	DNA	chemical	It was suggested that physical screening of DNA by protein shielded the DNA–protein interaction sites from radical damage, yielding an extended life-dose for the nucleoprotein complex compared with separate protein and DNA constituents at RT.	DISCUSS
+72	101	DNA–protein interaction sites	site	It was suggested that physical screening of DNA by protein shielded the DNA–protein interaction sites from radical damage, yielding an extended life-dose for the nucleoprotein complex compared with separate protein and DNA constituents at RT.	DISCUSS
+219	222	DNA	chemical	It was suggested that physical screening of DNA by protein shielded the DNA–protein interaction sites from radical damage, yielding an extended life-dose for the nucleoprotein complex compared with separate protein and DNA constituents at RT.	DISCUSS
+24	26	MX	experimental_method	However, in the current MX study at 100 K, the main damaging species are believed to be migrating LEEs and holes produced directly within the protein–RNA components or in closely associated solvent.	DISCUSS
+142	153	protein–RNA	complex_assembly	However, in the current MX study at 100 K, the main damaging species are believed to be migrating LEEs and holes produced directly within the protein–RNA components or in closely associated solvent.	DISCUSS
+62	75	nucleoprotein	complex_assembly	The results presented here suggest that biologically relevant nucleoprotein complexes also exhibit prolonged life-doses under the effect of LEE-induced structural changes, involving direct physical protection of key RNA-binding residues.	DISCUSS
+216	236	RNA-binding residues	site	The results presented here suggest that biologically relevant nucleoprotein complexes also exhibit prolonged life-doses under the effect of LEE-induced structural changes, involving direct physical protection of key RNA-binding residues.	DISCUSS
+93	98	bound	protein_state	Such reduced radiation-sensitivity in this case ensures that the interacting protein remains bound long enough to the RNA to complete its function, even whilst exposed to ionizing radiation.	DISCUSS
+118	121	RNA	chemical	Such reduced radiation-sensitivity in this case ensures that the interacting protein remains bound long enough to the RNA to complete its function, even whilst exposed to ionizing radiation.	DISCUSS
+11	19	nonbound	protein_state	Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸).	DISCUSS
+20	24	TRAP	complex_assembly	Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸).	DISCUSS
+82	104	RNA-binding interfaces	site	Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸).	DISCUSS
+106	111	Asp39	residue_name_number	Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸).	DISCUSS
+113	118	Glu36	residue_name_number	Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸).	DISCUSS
+120	125	Glu42	residue_name_number	Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸).	DISCUSS
+128	132	TRAP	complex_assembly	When exposed to X-rays, these residues will be preferentially damaged by X-rays and subsequently reduce the affinity with which TRAP binds to RNA.	DISCUSS
+142	145	RNA	chemical	When exposed to X-rays, these residues will be preferentially damaged by X-rays and subsequently reduce the affinity with which TRAP binds to RNA.	DISCUSS
+116	119	RNA	chemical	Within the cellular environment, this mechanism could reduce the risk that radiation-damaged proteins might bind to RNA, thus avoiding the detrimental introduction of incorrect DNA-repair, transcriptional and base-modification pathways.	DISCUSS
+177	180	DNA	chemical	Within the cellular environment, this mechanism could reduce the risk that radiation-damaged proteins might bind to RNA, thus avoiding the detrimental introduction of incorrect DNA-repair, transcriptional and base-modification pathways.	DISCUSS
+4	21	TRAP–(GAGUU)10GAG	complex_assembly	The TRAP–(GAGUU)10GAG complex asymmetric unit (PDB entry 1gtf; Hopcroft et al., 2002).	FIG
+0	5	Bound	protein_state	Bound tryptophan ligands are represented as coloured spheres.	FIG
+6	16	tryptophan	chemical	Bound tryptophan ligands are represented as coloured spheres.	FIG
+0	3	RNA	chemical	RNA is shown is yellow.	FIG
+62	70	TRAP–RNA	complex_assembly	(a) Electron-density loss sites as indicated by D loss in the TRAP–RNA complex crystal by residue/nucleotide type for five doses [sites determined above the 4× average D loss threshold, calculated over the TRAP–RNA structure for the first difference map: F obs(d 2) − F obs(d 1)].	FIG
+79	86	crystal	evidence	(a) Electron-density loss sites as indicated by D loss in the TRAP–RNA complex crystal by residue/nucleotide type for five doses [sites determined above the 4× average D loss threshold, calculated over the TRAP–RNA structure for the first difference map: F obs(d 2) − F obs(d 1)].	FIG
+206	214	TRAP–RNA	complex_assembly	(a) Electron-density loss sites as indicated by D loss in the TRAP–RNA complex crystal by residue/nucleotide type for five doses [sites determined above the 4× average D loss threshold, calculated over the TRAP–RNA structure for the first difference map: F obs(d 2) − F obs(d 1)].	FIG
+215	224	structure	evidence	(a) Electron-density loss sites as indicated by D loss in the TRAP–RNA complex crystal by residue/nucleotide type for five doses [sites determined above the 4× average D loss threshold, calculated over the TRAP–RNA structure for the first difference map: F obs(d 2) − F obs(d 1)].	FIG
+239	253	difference map	evidence	(a) Electron-density loss sites as indicated by D loss in the TRAP–RNA complex crystal by residue/nucleotide type for five doses [sites determined above the 4× average D loss threshold, calculated over the TRAP–RNA structure for the first difference map: F obs(d 2) − F obs(d 1)].	FIG
+72	75	DWD	evidence	(b) Average D loss for each residue/nucleotide type with respect to the DWD (diffraction-weighted dose; Zeldin, Brock­hauser et al., 2013).	FIG
+77	102	diffraction-weighted dose	evidence	(b) Average D loss for each residue/nucleotide type with respect to the DWD (diffraction-weighted dose; Zeldin, Brock­hauser et al., 2013).	FIG
+21	25	TRAP	complex_assembly	Only a subset of key TRAP residue types are included.	FIG
+46	50	TRAP	complex_assembly	The average D loss (calculated over the whole TRAP asymmetric unit) is shown at each dose (dashed line).	FIG
+13	31	difference density	evidence	In (a) clear difference density is observed around the Glu42 carboxyl side chain in chain H, within the lowest dose difference map at d 2 = 3.9 MGy.	FIG
+55	60	Glu42	residue_name_number	In (a) clear difference density is observed around the Glu42 carboxyl side chain in chain H, within the lowest dose difference map at d 2 = 3.9 MGy.	FIG
+104	130	lowest dose difference map	evidence	In (a) clear difference density is observed around the Glu42 carboxyl side chain in chain H, within the lowest dose difference map at d 2 = 3.9 MGy.	FIG
+130	133	RNA	chemical	Radiation-induced protein disordering is evident across the large dose range (b, c); in comparison, no clear deterioration of the RNA density was observed.	FIG
+134	141	density	evidence	Radiation-induced protein disordering is evident across the large dose range (b, c); in comparison, no clear deterioration of the RNA density was observed.	FIG
+53	56	Glu	residue_name	 D loss calculated for all side-chain carboxyl group Glu Cδ and Asp Cγ atoms within the TRAP–RNA complex for a dose of 19.3 MGy (d 8).	FIG
+64	67	Asp	residue_name	 D loss calculated for all side-chain carboxyl group Glu Cδ and Asp Cγ atoms within the TRAP–RNA complex for a dose of 19.3 MGy (d 8).	FIG
+88	96	TRAP–RNA	complex_assembly	 D loss calculated for all side-chain carboxyl group Glu Cδ and Asp Cγ atoms within the TRAP–RNA complex for a dose of 19.3 MGy (d 8).	FIG
+64	69	bound	protein_state	Residues have been grouped by amino-acid number, and split into bound and nonbound groupings, with each bar representing the mean calculated over 11 equivalent atoms around a TRAP ring.	FIG
+74	82	nonbound	protein_state	Residues have been grouped by amino-acid number, and split into bound and nonbound groupings, with each bar representing the mean calculated over 11 equivalent atoms around a TRAP ring.	FIG
+175	179	TRAP	complex_assembly	Residues have been grouped by amino-acid number, and split into bound and nonbound groupings, with each bar representing the mean calculated over 11 equivalent atoms around a TRAP ring.	FIG
+180	184	ring	structure_element	Residues have been grouped by amino-acid number, and split into bound and nonbound groupings, with each bar representing the mean calculated over 11 equivalent atoms around a TRAP ring.	FIG
+29	34	Glu36	residue_name_number	 D loss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms.	FIG
+43	48	Asp39	residue_name_number	 D loss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms.	FIG
+57	62	Glu42	residue_name_number	 D loss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms.	FIG
+72	77	Glu42	residue_name_number	 D loss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms.	FIG
+87	92	Phe32	residue_name_number	 D loss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms.	FIG
+104	109	Lys37	residue_name_number	 D loss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms.	FIG
+67	72	bound	protein_state	95% CI are included for each set of 11 equivalent atoms grouped as bound/nonbound.	FIG
+73	81	nonbound	protein_state	95% CI are included for each set of 11 equivalent atoms grouped as bound/nonbound.	FIG
+0	21	RNA-binding interface	site	RNA-binding interface interactions are shown for TRAP chain N, with the F obs(d 7) − F obs(d 1) Fourier difference map (dose 16.7 MGy) overlaid and contoured at a ±4σ level.	FIG
+49	53	TRAP	complex_assembly	RNA-binding interface interactions are shown for TRAP chain N, with the F obs(d 7) − F obs(d 1) Fourier difference map (dose 16.7 MGy) overlaid and contoured at a ±4σ level.	FIG