bluuebunny/crossref_metadata_2025 huggingface dataset:
Effective data collection and refinement of pertubated structures
Authors: Parois Pascal , Cooper Richard
Published: November 2015

Approaches to determining the influence of individual measurements on the precision of crystallographic least squares parameters have been known for a long while.[1] Situations in which the precision of a single parameter (or linear combination of parameters) is critical can include: determination of novel bond lengths; refinement of site occupancies in mixed metal or mixed oxidation state systems; determination of the fraction of excited state molecules in a time-resolved pump-probe experiment. Such calculations are easily applicable to point-detector instruments, where individual influential reflections could be remeasured one-by-one. However, on a modern area detector instrument many reflections are measured on one frame and therefore some consideration of the appropriate strategy of reciprocal space scans is permitted to allow a more efficient use of the instrument. The highly influential partial data collection is then feed into an appropriate refinement model. Occupancies in mixed-metal or mixed-oxidation state systems and fractions and positions of excited state molecules during a time-resolved pump-probe experiment can be determined using direct refinement of the perturbation of the structure from the ground state. Re-factoring to modern Fortran of the Crystals software is in progress to allow the implementation of new algorithms such as a difference refinement.[2] We present an analysis of diffractometer strategy selection to prioritize scans which give the best improvement in specific least-squares parameters and a novel algorithm for the refinement of the partial data using crystals.
Stock-based detection of biological assemblies in PISA software
Authors: Krissinel Eugene
Published: November 2015

PISA (Protein Interfaces, Surfaces and Assemblies) software from CCP4 remains a popular computational tool for the prediction of biological assemblies (complexes) from macromolecular crystallography data [1]. The method is based on the estimation of the dissociation free energy of predicted complexes, and reaches 90-95% correct results for the current content of the PDB. It was found that the probability of getting wrong predictions grows exponentially with the decrease in the dissociation free energy, reaching over 50% for complexes bound as weakly as few kcal/mol [2]. Among few reasons for this behaviour [2] is the fact that oligomeric state of weakly bound complexes is expected to vary in dependence of chemical environment, in particular, protein concentration. It has been noticed in multiple use cases, that a considerable share of disagreements between predicted and measured oligomeric states belongs to situations where the relation between experimental conditions and protein's working environment in the cell is unclear. We report further advance in PISA software, which allows a researcher to model concentration dependence of predicted oligomeric states, and by this to improve interpretation of both experiments and computations in the biologically interesting case of weakly bound macromolecular associations. The new PISA is based on the concept of assembly stock, which represents an equilibrated set of of all complexes, compatible with crystal packing. Graphical representation of concentration (or newly introduced aggregation index) profiles of stock's components allows a user to quickly identify the most probable oligomeric state. This is vastly superior over the previous way of analysis, based on the interpretation of bare figures for dissociation free energies. Other developments include advanced graphical interface and multi-parametric interaction radar, which indicates the likelihood for interface to represent a biologically-relevant interaction.
The State of the Canadian Macromolecular Crystallography Facility
Authors: Gorin James , Labiuk Shaunivan , Cotelesage Julien , Janzen Kathryn , Fodje Michel , Grochulski Pawel
Published: November 2015

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source consists of two macromolecular crystallography beamlines for structure determination using x-ray diffraction. The equipment at the CMCF beamlines have undergone or will undergo changes and improvements to better meet the needs of the most challenging experiments users may present. Among these improvements are: 1) Automounter improvements; 2) Better goniometry on 08ID-1 with the addition of a Huber air-bearing goniometer; 3) Added beam size capabilities on 08ID-1 with the addition of a multiple beam defining aperture holder; 4) XAFS capability on 08B1-1; 5) Improved low energy S-SAD data collection with the addition of a Helium path; 6) Improvements to the data collection and data management software; 7) A vacuum path for scattering experiments with detector distances up to 1 m; 8) A comprehensive beamline upgrade project on the 08ID-1 beamline; and 9) Service crystallography services.
Collecting data for several crystals in a single exposure to X-rays
Authors: Flores-Alamo Marcos , Maldonado-Hermenegildo Ana , Gómez-Ruiz Humberto
Published: November 2015

The experimental technique which has been of the greatest importance in revealing the structure of crystals is undoubtedly X-ray diffraction; recently with the CCD detector the time of collection data is most fast, which has given opportunity to explore the option of data collection multiple crystals or twinning crystals of same chemical substance. Considering the Ewald sphere or expression of Bragg's law where it involves the reciprocal lattice in the sphere of reflection and using CrysAlis PRO171 software [1] is possible to identify the number of unit-cells that are present in the material which is composed of multiple crystals (see figure) that have intentionally place in this work. By placing the [1,2-bis(diisopropylphosphanyl)ethane]dichloridonickel(II) (A)[2] and 17β-acetoxy-4,5-secoandrost-3-yn-5-one (B)[3] crystals in the X-ray diffractometer Gemini with Atlas area detector and source of radiation λMo.= 0.7103 to 130 K and collect data for the system of lowest symmetry (2) (laue group: mmm) obtained a total of 15341 reflections in 307 frames and 4 runs with a total time of 2h 17m. Using the lattice wizard tool and Ewald explorer-reciprocal space two groups of data collection is obtained, which the resolve and refine separately R1(obs data) of 0.0255 and 0.0574 for A and B compounds respectively.
Advanced Crystallographic Program at ChemMatCARS at Advanced Photon Source
Authors: Chen Yu-Sheng , Brewer Harold , Meron Mati , Viccaro Jim
Published: November 2015

ChemMatCARS, a state-of-the-art synchrotron-based national facility for Chemistry and Materials Science located at the Advanced Photon Source (APS), maintains dedicated advanced crystallographic programs for small molecule which include photo-crystallography, high resolution charge density studies, high pressure (<10 GPa) chemical crystallography using a diamond anvil cell(DAC), ultra-low temperature crystallography using open flow Helium at ~10 K, and element-specific resonant diffraction and diffraction anomalous fine structure (DAFS) (tunable energy from 5 to 70 keV). High throughput micro-crystallography benefits from a new sample preparation environment and a fast data collection strategy to enable measurements on air-sensitive samples in fewer than 5 minutes. This work is typically done by cooling the sample with cryogenic open flow nitrogen or helium. These new capabilities will impact the development of new materials to meet emerging challenges in energy, environment and life sciences. This poster focuses on the above scientific research activities and provides information on how to apply for beam time.
Hydrates of Silver(I) Fluoride and Zinc Chloride
Authors: Folkers Laura , Trapp Nils , Dunitz Jack , Wörle Michael
Published: November 2015

Hydrates of transition metal halides are routinely used in a wide range of applications as for example catalysts, electrolytes or heat storage materials[1] . The structural variety ranges from relatively simple structures with isolated coordination polyhedra to complex polymeric frameworks. Surprisingly, many of their crystal structures are still unknown. This is partially due to difficulties of growing and handling single crystals since the hydrates are often highly hygroscopic and deliquescent at ambient temperature. In order to prepare and systematically investigate these compounds by X-ray diffraction, the crystals have to be grown, selected and measured at low temperatures. Using a self-made device[2] to select and transfer the crystals while maintaining the cooling, we were able to grow suitable crystals and determine the structures of AgF·2H2O (trigonal bipyramidal coordination of Ag+ by 4 H2O and one F-), AgF·4H2O (octahedral coordination of Ag+ by 6 H2O) and ZnCl2·3H2O (octahedral coordination of Zn2+by 6 H2O and tetrahedral coordination by 4 Cl-).
Big Methods for Small Molecules
Authors: Sutton Karim , Cooper Richard , Allan David , Thompson Amber , Christensen Kirsten
Published: November 2015

Since the early 70's, multiple wavelength experiments have been used to determine phases of proteins containing anomalous scatterers. The small molecule single crystal beamline, I19,[1] at Diamond Light Source, is designed to carry out single crystal anomalous dispersion studies using tunable wavelength. These experiments can differentiate between oxidation states; discriminate between atoms with near-identical X-ray scattering factors; and solve the phase problem for very low resolution X-ray data. We describe the application of MAD phasing (Karle and Hendrickson [2]) to determine the structure of large `small molecules' where only low-resolution data is available. Initial studies were carried out on a known, (well diffracting) centrosymmetric bromide containing compound. The wavelength dependence of the anomalous signal from the bromide was calculated from fluorescence absorption data in DetOx.[3] Datasets were then collected at 4 wavelengths chosen to maximize differences in the anomalous signal. Using the MAD phasing equations we obtained estimates for the anomalous scattering contribution from all atoms in the structure and a phase difference between that and the normal scattering component. This allowed us to reduce noise in the Patterson map and locate only the heavy atom scatterers. We then use phase estimates from the heavy atom substructure to locate the rest of the atoms. Initial proof of concept experiments will now be extended to larger structures where data is not of sufficient resolution to be solved by direct methods alone.
Applications of Small Molecule Single Crystal Diffraction.
Authors: Staples Richard
Published: November 2015

IN the 20 plus years of performing small molecule single crystallography (SCXRD) I have seen many examples of how these results can influence chemistry and more important or understanding of the chemical world around us. I will present a number of applications where SCXRD has been an important tool in determining various aspects of the chemist understanding of the system they are studying. The range of topics will include identification, theory, reaction, and various other topics as time or space will present.
Single Crystal in Motion: An Insight into the Mechanism of Actuation
Authors: Panda Manas , Naumov Pance
Published: November 2015

Dynamic materials that can rapidly transform one form of energy into another have recently attracted attention because they could be utilized as platform for actuation from the nanoscale to the macroscale. This rapidly expanding field has brought up an increasing number of examples of oftentimes serendipitous observations of macro-, milli- and nano-sized single crystals that can hop, bend, curl or twist when exposed to light, heat or external pressure and have the capability to induce motion of other objects. Among these biomimetic crystalline actuators, the so-called thermosalient (TS) crystals, when heated or cooled, exhibit spectacular macroscopic motility as a result of fast coupling of thermal energy with mechanical actuation (Figure 1). Some of these crystals are exceptionally robust and undergo mechanical actuation for several cycles without disintegration. Achieving concurrently fast and reversible actuation of molecular crystals remains a great challenge since mechanical reconfiguration of single crystals is generally accompanied by loss of integrity (cracking, fracturing, explosion, etc.), a serious pitfall that limits their compatibility with the basic requirements for applications as dynamic modules. Despite the potential importance of these biomimetic crystalline actuators as smart materials, the detailed mechanism of actuation and shape change is not understood well. Here we report systematic investigation of the mechanism of mechanical response of these crystalline materials with the aid of single crystal X-ray diffraction, powder X-ray diffraction using synchrotron radiation, and other advanced instrumental techniques.
Crystal structures of two isostructural thiosemicarbazones and DFT calculations
Authors: Meroño Rafael , Granda Santiago , Merz Klaus , Saravanan R.R , Seshadri S. , Gunasekaran S.
Published: November 2015

The families of thiosemicarbazone compounds have been extensively studied due to their wide range potential in medical applications [1]. Some studies with acetophenone derivatives and their coordination complexes [2] reveal that these compounds could be used as a new class of anti-trypanosomal drug candidate. In view of the importance of these compounds, two new thiosemicarbazones (I) and (II) have been synthesized (compound I substituted with Chloro atom and compound II substituted with Bromine atom), and their crystal structure features are presented here. The crystal structures are isostructural and the molecules crystallize in a P21/c space group. In the crystal packing the molecules are connected through N-H···S hydrogen bonds to form a centrosymmetric synthon. The optimized geometry of the compound (I) was calculated from the DFT–B3LYP gradient calculations employing 6-31G (d,p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values. Molecular stability has been analyzed using Natural Bond Orbital (NBO) and Natural Localized Molecular Orbital (NLMO) analysis and the limits of the molecular electrostatic potential calculated. The HOMO and LUMO energies shows the charge transfer occurs within the molecule. The results showed no significant geometrical differences (distances and angles), when the solid state crystal structure is compared with the optimized structure in the gas phase. Very good agreements have been found between principal vibrational frequencies calculated from the optimized structure and the experimental spectroscopic data [3]. We thank financial support from Spanish Ministerio de Economía y Competitividad (MAT2010-15094, Factoría de Cristalización– Consolider Ingenio 2010, ERDF funds and German Academic Exchange Service (DAAD).
The changeable nature of urea inclusion compounds.
Authors: Lee Rachael , Probert Michael , Steed Jonathon
Published: November 2015

Urea inclusion compounds (UICs), the β-phase of urea, have been known only since 1949 and have revealed various structural and behavioural characteristics of interest, largely influenced by the type of guest molecule present in the crystal. These structures have a hexagonally symmetrical honeycomb structure of a hydrogen-bonded urea network encapsulating the guest molecules, a defining motif of these clathrates. The simplest of this class contains an alkane guest (C7-C20), creating an incommensurate relationship between host and guest and a significantly disordered crystal structure with respect to the guest. As a result, diffuse scattering is typical in the diffraction patterns of UICs. As the guest molecules are altered, so too is the behaviour of the host network. With certain dihaloalkanes for example, the guest may coil into an atypical conformation in order to present a commensurate relationship with the host. This increase in guest order creates a distortion of the host network away from hexagonal symmetry, creating an internal stress which causes domain switching within the system. A number of different effects such as this can be seen on changing the guest molecule, ferroelasticity being an example for certain diketone guests. In this work we are exploring examples of UICs which, due to unusual interaction between the host and guest, display atypical structural features, symmetry or behaviour. These crystal structures are under investigation at a range of temperatures and pressures, by both X-ray and neutron diffraction techniques in order to fully understand the nature and bonding of UICs.
Mole-Ratio-Dependent Supramolecular Isomerism in Ag(I) Coordination Networks
Authors: Lee Eunji , Lee Shim Sung , Park Ki-Min
Published: November 2015

Three regioisomers (o-L,m-L, andp-L) of bis(cyanobenzyl)sulfide were employed to examine the effect of ligand isomers on the networking assembly. In the reaction ofm-Lwith silver(I) nitrate, supramolecular isomers1and2of stoichiometry [Ag2(m-L)(NO3)2]n, each comprising a 2D polymeric network were obtained on varying the mole-ratio of the reactant (see the below scheme). Notably, the overall structural motifs of1and2are mainly due to the conformational differences of the tridentatem-L: `S-shaped' in isomer1and `V-shaped' in isomer2. Under identical reaction conditions, the ligand isomerso-Landp-Lyield a loop-chain type 1D coordination polymer [Ag(o-L)NO3]n(3) and a multichannel 3D framework structure [Ag2(p-L)(NO3)2]n(4), respectively. The formation of these products shows no mole-ratio dependency.1Among the ligand isomer,p-Lshowed the anion-dependent complexes5-7with different topologies in the reactions of silver(I) salts (X = ClO4-, PF6-, or CF3CO2-). AgClO4afforded a double-stranded 1D polymer of type [Ag(p-L)(ClO4)]n(5). Meanwhile, treatment of AgPF6and AgCF3CO2afforded a 2-fold interpenetrated 3D coordination polymer {[Ag3(p-L)4](PF6)3·4CH2Cl2}n(6) and a multichannel 3D network [Ag2(p-L)(CF3CO3)2]n(7), respectively.
Understanding complex phase transition mechanism by crystal structure analysis
Authors: Krūkle-Bērziņa Kristīne , Actiņš Andris
Published: November 2015

Xylazine hydrochloride (2-(2,6-xylidino)-5,6-dihydro-4H-1,3-thiazine hydrochloride) is an adrenergic α-agonist used as a sedative, analgesic, and muscle relaxant in veterinary medicine. It has four polymorphous forms (A, Z, M and X), monohydrate (H), hemihydrate and solvates with dichloromethane and 2-propanol. It has been reported that the polymorph X is thermodynamically the least stable of these polymorphs, while the A is the most stable form at temperatures above 500C. The X forms only in H dehydration process, and at elevated temperature X transforms to polymorph A [1]. The crystal structures of the polymorphs A and X as well as hydrate H have been reported. Crystal structure of A and X have been determined from the powder X-ray diffraction data (PXRD), whereas that of hydrate have been determined from single crystal X-ray diffraction data [2-3]. In this study structure of A have been determined from single crystal data and compared to that determined by PXRD data. Crystal structures of A, X and H have been compared and analysed. Molecule conformation in crystal structure of all three forms is the same and molecular packing is similar. However, that in monohydrate H and polymorph X is basically the same and the only difference is the inclusion of the water molecules next to the chlorine anions, whereas relative xylazine moiety orientation and arrangement of the chlorine anions is different in the structure of polymorph A. The structural similarity or differences between all three forms noted above were also approved by the 2D-fingerprint plots of the Hirshfeld surfaces. Analysis of all three form crystal structures allowed to better understand complex solid-state phase transition from xylazine hydrochloride polymorph X to polymorph A during and after the dehydration of it monohydrate H.
Mixed Alkaline Earth Germanides A2MGe2(A= Ca/Sr; M= Sn,Pb)
Authors: Jehle Michael , Langenmaier Michael , Steckhan Julia , Röhr Caroline
Published: November 2015

The crystal structures of the mixed alkaline earth tetrelides with the composition (CaxSr1-x)2MGe2 (M= Sn,Pb) exhibit identically stacked planes consisting of square planar coordinated M atoms (light gray) and [Ge]m zigzag chain pieces of varying lengths m. Each Ge atom is thereby coordinated by A atoms forming trigonal prisms (dark gray). The chain length m depends on the radius ratio rM4-/rA2+ (rr), whereat the M4- radius was estimated from the average Ca-M distances in the structures of Ca2M, which exhibit isolated tetrel anions. Depending on this radius ratio the structures of the title compounds feature [Ge]m chains of lengths m of 2, 4, 6 and infinite. Starting with Ge-Ge dumbbells in Ca2SnGe2 (rr= 1.57, space group P4/mbm, a= 748.58(13), c= 445.59)(8) pm, R1= 0.060, Mo2FeB2 type; cf. also Yb2SnGe2 [1], fig. top left), (Ca0.58Sr0.42)2SnGe2 shows Ge4 zigzag chain pieces (rr= 1.50, Pbam, a= 781.01(2), b= 1477.95(3), c= 457.00(1) pm, R1= 0.018, La2NiIn2 type; cf. also (Ca0.34Eu0.66)2PbGe2 [2], fig. bottom left). Ge6 pieces are present in (Ca0.23Sr0.77)2PbGe2 (rr= 1.48, Pbam, a= 2311.20(15), b= 791.64(5), c= 458.53(3) pm, R1= 0.073, new type, fig. top right) and infinit Ge chains in (CaxSr1-x)2PbGe2 (rr= 1.44-1.46, x= 0 to 0.22, Cmmm; for x= 0: a= 402.36(11), b= 1542.29(42), c= 463.27(10) pm, R1= 0.064, Mn2AlB2 type; cf. also (Sr0.21Eu0.79)2PbGe2 [2], fig. bottom right). In this series, i.e. with increasing m, the connectivity of M changes from a square planar coordination by four Ge in Ca2SnGe2 ([MGe4]) via [MGe3M] in (Ca0.58Sr0.42)2SnGe2 and [MGe3M]2[MGe2M2] in (Ca0.23Sr0.77)2PbGe2 up to [MGe2M2] in Sr2PbGe2, finally. The details of chemical bonding are discussed on the basis of band structure calculations.
Bonding modes of some labile Si compounds studied by charge density analysis
Authors: Hashizume Daisuke
Published: November 2015

Some organic molecules containing Si atom(s) are very labile, even if the corresponding carbon analogs are very stable. To gain information on bonding modes of such compounds, we analyzed valence density distribution, which play critical roles in chemistry of molecule, by applying multipole expansion method. Very recently, an imine coordinated silacyclopropan-1-one, 1, has synthesized by Baceiredo, Kato and co-workers.[1] To clarify the bonding mode of 1, the electron density distributions of 1 and its precursor have analyzed by a multiple expansion method using single crystal X-ray diffraction data. As shown in static model density maps, bonding electrons of Si-C bonds distribute on the outside of the silacyclopropane ring (Si1-C1-C2 ring) (Fig. 1a) with largely extent, in compared with that of the precursor, indicating an in-plane pi-interaction on the Si1-C1 and Si1-C2 bonds. On the other hand, the C1-C2 bonding electrons distribute on the bond, and the bond critical point (BCP) is located on the inside of the three membered ring. In addition, the C1-C2 bonding electrons elongates inside the ring toward the Si1 atom, indicating electron donation from sigma(C1-C2)-bond to the Si1 (Fig. 1b). Consequently, these maps propose greater contribution of canonical structures in Fig. 1c.
Crystallographic approach to determination of active conformations of LCAPs
Authors: Glowka Marek , Szczesio Malgorzata , Olczak Andrzej
Published: November 2015

Long-Chain Aryl-Piperazines (LCAPs) are well known serotonin receptor ligands used in several marketed antidepressant drugs. LCAPs consist of three structural units: a terminal group, an arylpiperazine at one N atom and an aliphatic chain (spacer) at the other N atom joining the two former units. Both the arylpiperazine and the terminal groups have rather rigid structures and thus their conformational freedom is limited. The opposite is true for the aliphatic spacer, which allows practically any orientation of the terminal group. The resulting diversity of conformations observed in the crystals of LCAPs is significant, which explains their affinity to many serotonin receptors. There is a vast literature on the subject and some qualitative observations were developed. However, due to the flexible spacer and diversity of the terminal groups, their usefulness is limited. Our X-ray (16 crystal structures) and affinity studies on almost sixty new LCAPs [1], together with the data from CSD, enable us to determine the common conformations of LCAPs and the relationships between structure, affinity and conformation. In the analysis, the following features were considered: (i) - axial/equatorial orientations of the substituents of the piperazine ring; (ii) –N1 protonation possible in the physiological environment; (iii) - a twist of the aryl ring; (iv) –the parity and the number of atoms in the spacer; (v) – the presence of heteroatoms or groups in the spacer; (vi) – the spatial position of the terminal group in relation to the piperazine ring.
Elucidating Chemical Structure at Station 11.3.1 at the Advanced Light Source
Authors: Gagnon Kevin , Beavers Christine , Morrison Gregory , Nasiatka James , Teat Simon
Published: November 2015

One of the greatest challenges facing crystallographers has always been how to collect good data. This has become especially challenging as chemists are creating more complex compounds and looking to extract new exotic structural information from crystals which are getting smaller and smaller. Often, these crystals produce little or no diffraction on a laboratory diffractometer with long exposures. The past two decades have provided world-class synchrotron facilities to help solve these problems through a combination of high flux and a small focused beam spot size. Station 11.3.1 at the Advanced Light Source is a dedicated chemical crystallography beamline which has been developed and improved over the last decade to provide a global user base with a high flux, focused beam which is capable of doing more than just providing excellent data on weakly diffracting samples. Recent developments on station 11.3.1 include an environmental gas cell for studying of samples under evacuation, up to 1 atm of gasses and mixtures of gasses, and under gas flow; a diamond anvil cell for studying samples under applied pressures up to 10 GPa, a photodiode array for in-situ photocrystallography, as well as a tunable monochromator allowing energies between 6.5 and 22 keV. This poster will showcase the recent changes to station 11.3.1 as well as the future plans for upgrades.
Opening up the Lab Notebook: Publishing Experimental & Supplementary Information
Authors: Coles Simon , Tizzard Graham , Kuras Jan
Published: November 2015

Supplementary Information supporting publications is not uniform across journals, is generally not 100% representative of the work undertaken, is not structured or comprehensive and therefore is often not fully considered in review. In chemistry articles where characterisation techniques are applied widely, crystallography is the exception in that there are universally agreed processes and protocols for presenting the scientific findings and the supporting data. Crystallography can therefore lead the way! Our approach to solving the broader problem of availability of supporting information is to expose the observations of the researchers who conducted the work when it was performed. By combining these observations with related data (eg in information management systems) and linking these with the article there is the potential for a much richer system for data supporting a publication. The Electronic Laboratory Notebook (ELN) plays a key role by establishing authenticity, adding structure to the record and having the capacity to be made open. We present a formal publication in Chemistry Central Journal (http://journal.chemistrycentral.com/content/7/1/182) which is a collaborative piece of work between the UK National Crystallography Service (University of Southampton) and the University of Greenwich, where the data supporting the article is not contained within it, but is openly exposed at source by an ELN and a crystal structure repository. We draw on the experience of crystallographic publishing and aligning that with the other characterisation techniques alongside which crystal structures are routinely published and related. The article presents all the supplementary information (some 35 or so data sources) in a single graphical approach, which permits examination of synthesis, spectra & structures in-line and provides a link to the original ELN record. All records are assigned a Digital Object Identifier (DOI) by a system established within the University.
The solvent effect on the crystal morphology of two tegafur polymorphs
Authors: Bobrovs Raitis , Mitriķe Līga , Actiņš Andris
Published: November 2015

Pharmaceutical compounds are mostly produced in defined crystalline forms that are usually crystallized from solutions. Polymorphs, different crystalline phases of the same pharmaceutical compound, usually have different, precisely known dissolution rates and bioavailability, but crystal size and shape can affect these properties. Therefore, the crystal shape is monitored during the drug manufacturing process and a lot of work in the area of crystal engineering has been devoted to crystal habit control [1]. The crystallization solvent can have a significant effect on the resulting crystal shape; therefore solvent effect on crystal habit needs comprehensive studies. The compound studied in this research – tegafur (5-fluoro-1-(tetrahydro-2-furyl)-uracil) – is an antitumor agent, known to exist in α, β, γ, δ and ε polymorphs [2, 3]. Single crystal X-ray diffraction (SC XRD) was used to index crystal faces of α and β tegafur crystals grown in different solvents and molecular dynamics (MD) simulation was used as a tool to estimate the crystal face growth rates in several solvents. SC XRD results indicated that {011} and {110} faces dominated in β tegafur crystals when crystallized from ethanol, methanol, butyl acetate, tetrahydrofuran, whereas α tegafur crystals had a dominant {001}, {010} and {011} faces when crystallized from these solvents. Crystals grown in acetone had a different dominant faces for both polymorphs. The interaction between the solvents and each tegafur face was different, but the order of binding energy on these surfaces remained the same and was {011} > {110} > {010} for β tegafur and {001} > {011} > {010} for α tegafur. The analysis of MD data revealed that the system's primary interactions are weak hydrogen bonds. The achieved predictions were in agreement with experimental results. This work has been supported by the European Social Fund within the project «Support for Doctoral Studies at University of Latvia».
Crystal structure of Msm Eis bound with paromomycin
Authors: Yoon Hye Jin , Kim Kyoung Hoon , Suh Se Won
Published: November 2015

The Rv2416c gene of Mycobacterium tuberculosis (Mtb) encodes the enhanced intracellular survival (Eis) protein that enhances intracellular survival of the pathogen in host macrophages during infection. The Eis protein is secreted by Mtb into the cytoplasm of the phagocyte during intracellular infection and modulates the host immune response. It was shown to confer resistance to aminoglycosides by acetylation. Interestingly, nonpathogenic Mycobacterium smegmatis (Msm) contains a homologous eis gene (MSMEG_3513) that encodes a homolog of Mtb Eis. We discovered that Mtb Eis is an Nε-acetyltransferase, acetylating Lys55 of DUSP16/MKP-7, a JNK-specific phosphatase, whereas Msm Eis is an Nα-acetyltransferase (Kim et al., 2012). We also reported that Msm Eis acetylated the aminoglycosides as quickly as, or more rapidly than, Mtb Eis (Kim et al., 2012). Here we present the crystal structure of Msm Eis in the paromomycin-bound form. This structure provides a detailed structural view of the interactions between paromomycin and Msm Eis. Glu137 and Gly401 of Msm Eis are key residues that interact with paromomycin. Our work may facilitate a structure-guided discovery of Mtb Eis inhibitors as a novel anti-TB drug.
IPR Beamline for Macromolecular Assemblies at SPring-8 (BL44XU)
Authors: Yamashita Eiki , Higashiura Akifumi , Yoshimura Masato , Hasegawa Kazuya , Furukawa Yukito , Ohata Toru , Kumasaka Takashi , Ueno Go , Yamamoto Masaki , Nakagawa Atsushi
Published: November 2015

Biological macromolecular assemblies play significant roles in many biological reaction systems, including energy transfer, protein synthesis, protein degradation and signal transduction. A detailed understanding of the functions of the macromolecular assemblies requires information derived from three-dimensional atomic structures. X-ray crystal structure analysis is one of the most powerful methods to determine the three-dimensional structures of macromolecular assemblies at atomic level. Since features of crystals of biological macromolecular assemblies are extremely weak diffraction power and narrow space between the diffraction spots, it is essential to use high brilliance and high paralleled synchrotron radiation for diffraction data collection from crystals of biological macromolecular assemblies. The Institute for Protein Research (IPR) of Osaka University is operating a beamline for crystal structure analysis of biological macromolecular assemblies at SPring-8 (BL44XU). This beamline is designed to collect high quality diffraction data from biological macromolecular assembly crystals with large unit cells. The light source of this beamline is a SPring-8 standard type in-vacuum undulator. Liquid nitrogen cooled double crystal monochromator and horizontal focusing mirror are used as the optical components. BSS (Beamline Scheduling Software), which is SPring-8 protein crystallography beamline standard GUI, is installed to unify user operation throughout protein crystallography beamlines in the SPring-8. We have recently upgraded to a high speed air-bearing goniostat and installed a high performance CCD detector, MX-300HE. Present status and future plan of the beamline will be presented.
The organomercurial lyase Merb possesses unique metal-binding properties
Authors: Wahba Haytham , Mansour Ahmed , Vanasse Julien , Cappadocia Laurent , Sygusch Jurgen , Wilkinson Kevin , Omichinski James
Published: November 2015

Select bacterial strains survive in mercury-contaminated environments due to acquisition of a transferable genetic element known as the mer operon. The mer operon typically encodes for a series of proteins that includes two enzymes, MerA and MerB. The organomercurial lyase (MerB) cleaves carbon-mercury bonds of organomercurial compounds yielding ionic mercury Hg (II) and a reduced-carbon compound. The Hg (II) ion product remains bounds until it is shuttled directly to the mercuric ion reductase (MerA) to be reduced. Based on NMR spectroscopy and X-ray crystallography studies1, we have determined that Cys96, Asp99 and Cys159 of E. Coli MerB form a catalytic triad required for cleavage of the carbon-Hg bond and binding of the Hg (II) ion product. The three catalytic residues are conserved in 61 of 65 known variants of MerB and the four remaining variants retain both cysteine residues, but contain a serine in place of Asp99. Given its unique activity, we have examined the role of serine as a catalytic residue and the ability of MerB to cleave other organometals such as organotin (known substrates or inhibitors) and organolead compounds. Soaking MerB crystals with either dimethyltindibromide or trimethylleadchloride compound indicates that MerB crystals have the capacity to cleave both carbon-Sn and carbon-Pb bonds, and we have determined crystal structures of a MerB-Sn and a MerB-Pb complex. Furthermore, substitution of Ser for Asp99 (MerB D99S) in E. coli MerB alters the metal-binding specificity, as MerB D99S chelated an unknown metal during its purification. X-ray crystallography, ICP-MS and electron paramagnetic resonance (EPR) studies were performed to identify the unknown metal and the results of these studies will be presented. Given that mercury contaminated sites are often contaminated with other heavy metals, these studies indicate that other heavy metals may have important implications when using MerA and MerB in bioremediation of organomercurial compounds.
Structure-function studies of CrmK, an oxidase involved in Caerulomycin A biosynthesis
Authors: Picard Marie-Ève , Barma Julie , Zhu Yiguang , Murphy Després Xavier , Duvignaud Jean-Baptiste , Zhang Changsheng , Shi Rong
Published: November 2015

Caerulomycin A (CRM A) is an immunosupressive agent that has a unique 2,2'-bipyridine core structure. Isolated from a marine-derived Actinoalloteichus cyanogriseus, this natural product exhibits antifungal, anti-amoebic, antitumor, and antimicrobial activities. Its biosynthetic pathway consists of more than 20 enzymes, at least seven of which are putatively involved in post-PKS/NRPS modifications of the scaffold. Among these, CrmK is a flavin-dependent oxidase. We have determined the crystal structure of CrmK bound to its flavin adenin dinucleotide (FAD) cofactor at 1.9 Å resolution. FAD linkage to CrmK is observed via two covalent bonds with protein residues His64 and Cys124. This crystal structure, combined with the activity analysis of both wild-type CrmK and a series of mutants, has revealed the role of active site residues lining the substrate and FAD binding pocket. Our studies add additional molecular insights into the structure and function relationship of the bicovalently flavinylated oxidases.
Crystal structure of isocitrate lyase from Magnaporthe grisea
Authors: Park Yangshin , Rhee Sangkee
Published: November 2015

Glyoxylate cycle is a branched metabolic pathway in the TCA cycle that was initially discovered in microorganisms. The branched cycle plays an essential role in those organisms by providing the means for microorganisms to utilize acetate, ethanol, or fatty acids as carbon sources. In fact, pathogenic microorganisms rely on the glyoxylate cycle, rather than the TCA cycle, during infection. Therefore, the enzymes in the glyoxylate cycle of pathogens were suggested to be one of drug target molecules. Magnaporthe grisea isocitrate lyase (MgICL), a key enzyme in the cycle, is highly expressed during appressorium-mediated plant infection. In order to characterize the structural and functional features of MgICL, a structure of MgICL was determined at 2.7 Å resolution by X-ray crystallography. Recently, we are carrying out structure determination of MgICL in complex with a possible candidate for inhibitors. Our study could provide detailed structural features of MgICL and the binding mode of an inhibitor. This work was supported by a grant from Center for Fungal Pathogenesis by National Research Foundation, Republic of Korea.
Structural study of the Schiff base copper(II) chelates as thrombin inhibitor
Authors: Okada Chiaki , Hatae Noriyuki , Toyota Eiko
Published: November 2015

Thrombin is a trypsin-like serine protease that plays a critical role in the blood coagulation cascade. Thus, studies on thrombin-specific inhibitor are useful for the design of clinical useful compounds. We have previously reported of the Schiff base metal chelates carrying benzamidine and amino acid moieties. More than 50 kinds of Schiff base copper(II) chelates were synthesized fromp- orm-amidinosalicylaldehyde and various L- or D-amino acids. These chelates have effective inhibitory activity for trypsin and thrombin (Ki= 10-5~ 10-6M). In this series of inhibitors, the copper(II) chelate derived fromp-amidinosalicylaldehyde and D-tryptophan (chelate1g'in original paper) have shown exceptionally potent inhibitory activity against thrombin (Ki= 2.7×10-8M). To elucidate the structural basis of this high efficient inhibition, we were planning to determine and compare with four protein-inhibitor complex structures, chelate1g'or2g'bound to trypsin or thrombin (chelate2g'is derived fromm-amidinosalicylaldehyde and D-Trp). The crystals of trypsin binding the chelate2g'was obtained by sitting-drop vapor diffusion method by mixing 2.5 μL of 20 mg/mL protein-chelate complex solution with 2.5 μL of 0.1 M HEPES, pH 7.4, containing 0.1 M Li2(SO4), 25.0% PEG 3350. In the crystal structure, the imidazole nitrogen of His57 is coordinated with the copper(II) ion (1.94 Å). This close contact is made possible by conformation change of the His57. The indole ring of the chelate2g'simultaneously interacts with the copper(II) and the His57 by cation-π and π-π stacking interaction, respectively. In addition to trypsin-chelate2g'complex structure, we will report on the other three complex structures of trypsin-chelate1g', thrombin-chelate1g'and thrombin-chelate2g'.
Structural basis for bacterial quorum sensing-mediated oxalogenesis
Authors: Oh Juntaek , Goo Eunhye , Hwang Ingyu , Rhee Sangkee
Published: November 2015

Bacterial quorum sensing (QS), a cell-to-cell communication process in many Proteobacteria, controls the gene expression for bacterial population-wide characteristics, including bioluminescence, motility, and virulence-related factors. Recently, QS has been recognized to provide further benefits at the population level by regulating the production of public goods, the function of which could be beneficial to all members of the group. In Burkholderia species, oxalic acid was recently identified as an excreted public good for the QS-dependent growth. In these species, QS-mediated oxalogenesis via the oxalate biosynthetic component (obc) is a cellular event indispensable for the survival of bacteria in the stationary phase. Specifically, the acidity of the oxalic acid produced regulates the pH of the environment, avoiding a possible sudden collapse of the bacterial population caused by an alkaline pH in the stationary phase of their growth. In B. glumae, obc consists of two genes encoding ObcA and ObcB for coordinating the production of oxalic acid, as well as acetoacetate and CoA, by using oxaloacetate and acetyl-CoA as substrates. In contrast, the two substrates are also utilized by citrate synthase in the TCA cycle. To investigate any structural and functional differences between ObcA and citrate synthase, we are now carrying out structural and functional analysis of ObcA. Here, we will report our progresses on crystallization and structure determination of ObcA from B. glumae. Our analyses will provide structural insights into the first step in oxalogenesis and the mechanistic features of ObcA.
Automated High-Throughput Data Collection at IMCA-CAT
Authors: Mulichak Anne , Battaile Kevin , Digilio Joe , Muir J. Lewis , Zoellner Eric , Keefe Lisa
Published: November 2015

The Industrial Macromolecular Crystallography Association Collaborative Access Team (IMCA-CAT) operates a data collection facility at the Advanced Photon Source for protein crystallography. IMCA-CAT meets the demands of IMCA member pharmaceutical companies for reliable, high-quality, high-throughput data collection, while ensuring a secure environment for proprietary research. The 17ID micro-focused high-flux insertion device beamline, equipped with a Pilatus 6M pixel array detector, allows for very fast data collection times. The focused beam size (30 μm x 70 μm) can be easily optimized for each sample using a GM/CA-CAT mini-beam quad collimator, with user-selectable beam sizes of 50, 20, 10 and 5 μm. An Alio goniometer has a small (1.2 μm) sphere of confusion, providing stable sample positioning, and X-ray beam position is maintained within 2 μm by custom software in real time. Automated sample mounting is performed with a Rigaku ACTOR robot, accepting both Rigaku and ALS/Unipuck style magazines, providing fast yet reliable sample exchanges and enabling remote access and unattended data collection. Rigaku JDirector software for robot control and data collection has been customized to incorporate additional tools, such as diffraction-based sample centering for both manual and unattended data collection modes, vector data collection and inverse beam anomalous data collection. While targeting the needs of industrial research, the automation and rapid data collection times at 17ID are also ideally suited for structural genomics and other research efforts requiring high-throughput experiments. Access is available to interested researchers through the APS General User Program and through subscription memberships for those needing regular and guaranteed proprietary beamtime.
Visualizing soaking process of protein crystal
Authors: Mizutani Ryuta , Shimizu Yusuke , Saiga Rino , Ueno Go , Nakamura Yuki , Takeuchi Akihisa , Uesugi Kentaro , Suzuki Yoshio
Published: November 2015

Time-resolved visualization of the soaking process of tetragonal lysozyme crystal was performed by synchrotron radiation microtomography. Mother liquor containing hexachloroplatinate was introduced into a capillary bearing lysozyme crystals to visualize crystals undergoing soaking. The platinum distribution was first observed in the superficial layer of crystal and then gradually penetrated into the crystal core. The crystal structure of the platinum derivative in each soaking period was determined by time-resolved crystallography. A total of five platinum sites were identified in Bijvoet difference maps. These sites were classified into two groups on the basis of the time dependence of electron density development. A soaking process model consisting of binding-rate-driven and equilibrium-driven layers is proposed to describe the results. This study suggests that the structures of soaked crystals vary depending on the crystal position from which diffractions were taken.
Structure basis for E2-E3 interaction in the plant Atg conjugation system
Authors: Matoba Kazuaki , Fujioka Yuko , Sakoh-Nakatogawa Machiko , Nakatogawa Hitoshi , Ohsumi Yoshinori , Noda Nobuo
Published: November 2015

Autophagy is an intracellular degradation system conserved from yeast to mammal that isolates the cellular materials and organelles into a double membrane vesicle, termed an autophagosome, for degradation. Autophagosome formation depends on Atg8 and Atg12 conjugation systems, which produce Atg8-phosphatidylethanolamine (PE) conjugate as a final product that plays a crucial role for promoting autophagy. Another conjugate, Atg12-Atg5, functions as E3 and promotes transfer of Atg8 from Atg3 (E2) to PE. Here, we identified the minimum binding region of Atg3 for Atg12 by in vitro pull-down assay using Arabidopsis thaliana (At) homologs and crystallized the AtAtg12b-AtAtg3 peptide complex. The obtained crystal (P64, a = 128.5, b = 128.5, c = 163.2 Å) diffracted X-rays to 3.2 Å resolution, and its structure was determined by the molecular replacement method. AtAtg12b forms a swapping dimer in the crystal. The side-chain of AtAtg3 Met157 is bound deeply to the hydrophobic pocket of AtAtg12b consisting of Phe30, Val41, and Phe44. The importance of AtAtg3 Met157 for AtAtg12b binding was confirmed by mutational analysis. These data establish the basis for E2-E3 interaction in the plant Atg system.