bluuebunny/crossref_metadata_2025 huggingface dataset:
Nine isomeric nitrobenzylidene-iodoanilines: interplay of C—H...O hydrogen bonds, iodo...nitro interactions and aromatic π...π stacking interactions
Authors: Glidewell Christopher , Howie R. Alan , Low John N. , Skakle Janet M. S. , Wardell Solange M. S. V. , Wardell James L.
Published: September 2002

Nine isomeric nitrobenzylidene-iodoanilines, O2NC6H4CH= NC6H4I [(I)–(IX)], have been synthesized and the structures of all except 4-nitrobenzylidene-4′-iodoaniline (IX) have been analyzed. 2-Nitrobenzylidene-2′-iodoaniline (I) contains isolated molecules, while 3-nitrobenzylidene-2′-iodoaniline (II) and 2-nitrobenzylidene-3′-iodoaniline (IV) both contain chains of molecules linked by C—H...O hydrogen bonds: similar chains in 4-nitrobenzylidene-2′-iodoaniline (III) are further linked by aromatic π...π stacking interactions, forming sheets. In both 3-nitrobenzylidene-3′-iodoaniline and 4-nitrobenzylidene-3′-iodoaniline, (V) and (VI), a combination of C—H...O hydrogen bonds and iodo...nitro interactions generates molecular ladders that are linked into sheets by aromatic π...π stacking interactions, while in 2-nitrobenzylidene-4′-iodoaniline and 3-nitrobenzylidene-4′-iodoaniline, (VII) and (VIII), which both crystallize with Z′ = 2 in C2/c and P\bar 1, respectively, the combination of C—H...O hydrogen bonds and iodo...nitro interactions generates sheets, which in (VIII) are further linked by π...π stacking interactions to form a three-dimensional structure. The 4,4′-isomer (IX) crystallizes in Fdd2 with Z′ = 2, but both molecules are intractably disordered.
Synthesis, properties and X-ray crystal structure of a new heteropolyacid supermolecular charge-transfer complex [(VB1)2DMFHPMo12O40·5DMF]
Authors: Liu Shizhong , Li Jianping , Feng Xianhua , Cao Zhengtai , Zhang Zhenwen , Wang Zheng , Xing Yan , Jia Hengqing , Lin Yonghua
Published: September 2002

The title complex [(VB1)2DMFHPMo12O40·5DMF, VB1 = vitamin B1 (thiamine chloride), DMF = N,N-dimethylformamide] has been synthesized and characterized by elemental analysis, IR, UV-Vis, electron spin resonance, X-ray photoelectron spectroscopy and cyclic voltammetry methods. The X-ray crystal structure revealed that there is one independent molecule in the unit cell of the title complex that contains one mixed-valence heteropolyanion, two VB1
+ cations and six DMF molecules. The title complex possesses a centrosymmetrical arrangement in the unit cell, with the P atom at the symmetry center of the heteropolyanion and with eight O atoms surrounding the central P atom, such that two sets of PO4 tetrahedra are formed. The PO4 tetrahedra and MoO6
6−(7−) octahedra are disordered in the heteropolyanion. The bond distances of P—O
a
and Mo=O
d
are in the ranges 1.57 (4)–1.70 (4) Å and 1.61 (2)–1.67 (2) Å, respectively.
Some errors from the crystallographic literature, some amplifications and a questionable result
Authors: Herbstein Frank H. , Hu Shengzhi , Kapon Moshe
Published: September 2002

The space groups of {[Mo2(O2CCH3)4(`linker')]
n
} are corrected from P\bar 1 to C2/m for `linker' = pyrazine and 1,4-diazabicyclo[2.2.2]octane (dabco) and from P\bar 1 to C2/c for `linker' = 4,4′-bipyridine. Also, {[tris-(2-pyridylmethyl)amine]BrV(μ-O)VBr[tris-(2-pyridylmethyl)amine]}Br·H2O is corrected from P\bar1 to C2/c. These Laue class changes allow more reliable crystallochemical comparisons to be made among families of related structures. Space groups are correctedfor 4-methyl-2,6-bis(4-methylbenzylidene)cyclohexanone, 2,6-bis(4-dimethylaminobenzylidene)cyclohexanone, K[Cr(tetramethylenediamine-N,N,N′,N′-tetraacetate)]·H2O and {bis(11,-11-dimethyl-3,4:8,9-dibenzobicyclo[4.4.1]undeca-3,8-diene)-(tetracyanoethylene)}. The conflicting reports for Cu(H2O)-(phenanthroline)2(X)2, where X = ClO4, NO3 and BF4, are resolved. Three related examples of open framework host–guest structures with space groups `Cc or C2/c' are discussed. Adding centers to 2,2′-bi-1H-imidazolium dipicrate and {tris(2,2′-bi-1H-imidazole)bis[2-(2-1H-imidazolyl)-1H-imidazolium]bis(iodide)} corrects discrepancies of up to 0.38 Å between chemically similar hydrogen-bond distances. Wrongly identified atoms are corrected in θ-[bis(ethylenedithio)tetrathiafulvalene]2 (CsCd)(SCN)4 and (purported) diaquadihydroxotetrakis(m-nitrobenzenesulfonate)discandium(III). The reported difference between the crystal structure of (CH3NH3)4YbCl7 and those of the other members of this family of (CH3NH3)4
MX
7 (M = In, Fe, V; X = Cl, Br) structures is pointed out in the context of possibly different N—H...Cl hydrogen bonding in the Yb structure.
Bond angles and bond lengths in monosubstituted benzene and ethene derivatives: a comparison of computational and crystallographic results
Authors: Exner Otto , Böhm Stanislav
Published: September 2002

Bond angles and bond lengths in 29 monosubstituted benzene derivatives and in the same number of ethene derivatives were calculated at the B3LYP/6-311+G(d,p) level. Angle deformations in benzene derivatives agree reasonably with those derived statistically from the crystallographic data; in the case of small deformations, the calculated parameters are even more reliable. There is little correlation between geometry and reactivity parameters (σ-constants) in spite of some previous claims. Nevertheless, three components of the substitution effect can be distinguished: (a) strong deformation of the adjoining angles and bonds can be ascribed to changes of hybridization; (b) a weaker effect in the meta and para positions is only partially related to resonance; (c) in the case of unsymmetrical substituents, the symmetry of the benzene ring is also broken – the angular group-induced bond alternation (AGIBA) effect. The latter effect was also confirmed by searches in the Cambridge Structural Database for alkoxy, alkylthio, acyl and azo derivatives.
Location of the H atoms in ammonium persulphate by deuteron NMR. Verification by X-ray diffraction
Authors: Schmidt Thorsten , Schmitt Heike , Zimmermann Herbert , Haeberlen Ulrich , Lalowicz Zdzisław T. , Olejniczak Zbigniew , Oeser Thomas
Published: September 2002

It is demonstrated that H atoms can be located by the spectroscopic method of deuteron NMR. The requirement is that the `heavy-atom' positions are known from diffraction studies. The technique allows an accuracy of the order of 0.01 Å. The compound studied is ammonium persulphate (APS), (NH_4)_2S_2O_8. APS crystallizes in space group P2_1/n with lattice parameters a = 6.1340 (2), b = 7.9324 (3), c = 7.7541 (3) Å and \beta = 94.966 (1)° at T = 118 K. In perdeuterated crystals of APS, only one of the deuterons of every ND^+_4 ion becomes localized at low temperatures. Therefore, most of this work uses samples with 9% deuteration. In such crystals, most of the ammonium ions containing deuterons come in the form of NDH^+_3 ions. At T \,\lt\, 25 K, the single deuteron of these ions becomes localized in one of four equilibrium sites. The deuteron site occupancies differ from each other and are measured at 17 K. The deuterons are located in three steps. (i) The deuteron quadrupole-coupling (QC) tensors are measured at 17 K. Their unique principal directions are identified, as is well justified, with the N—D bond directions. (ii) The fine structure of a deuteron NMR line is analyzed in terms of the magnetic dipole–dipole interactions between all nuclei in an NDH^+_3 ion to obtain the N—D and D—H internuclear distances. (iii) An empirical relation between deuteron QC constants and D\cdotsO distances in N—D\cdotsO hydrogen bonds is exploited to assign the N—D bond vectors to the appropriate N atom of which there are four in the unit cell. The results are highly relevant for an understanding of the complex tunnelling and stochastic reorientation dynamics of the ammonium ions in APS. They are verified by a complementary X-ray diffraction study.
The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base
Authors: Nowell Harriott , Attfield J. Paul , Cole Jason C.
Published: September 2002

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C10H12N2), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P212121, a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) Å, Z = 4, final reduced-χ2 = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on χ2 was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.
The space groups of point group C
3: some corrections, some comments
Authors: Marsh Richard E.
Published: September 2002

A survey of the October 2001 release of the Cambridge Structural Database [Cambridge Structural Database (1992). Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, England] has uncovered approximately 675 separate apparently reliable entries under space groups P3, P3_1, P3_2 and R3; in approximately 100 of these entries, the space-group assignment appears to be incorrect. Other features of these space groups are also discussed.
Structures of three substituted arenesulfonamides from X-ray powder diffraction data using the differential evolution technique
Authors: Tremayne Maryjane , Seaton Colin C. , Glidewell Christopher
Published: September 2002

The structures of three substituted arenesulfonamides have been solved from laboratory X-ray powder diffraction data, using a new direct-space structure solution method based on a differential evolution algorithm, and refined by the Rietveld method. In 2-toluenesulfonamide, C7H9NO2S (I) (tetragonal I41/a, Z = 16), the molecules are linked by N—H...O=S hydrogen bonds into a three-dimensional framework. In 3-nitrobenzenesulfonamide, C6H6N2O4S (II) (monoclinic P21, Z = 2), N—H...O=S hydrogen bonds produce molecular ladders, which are linked into sheets by C—H...O=S hydrogen bonds: the nitro group does not participate in the hydrogen bonding. Molecules of 4-nitrobenzenesulfonamide, C6H6N2O4S (III) (monoclinic P21/n, Z = 4), are linked into sheets by four types of hydrogen bond, N—H...O=S, N—H...O(nitro), C—H...O=S and C—H...O(nitro), and the sheets are weakly linked by aromatic π...π stacking interactions.
An exceptionally stable peptide nanotube system with flexible pores
Authors: Görbitz Carl Henrik
Published: September 2002

The hydrophobic channels in the structure of the dipeptide L-alanyl-L-valine act as supramolecular hosts for organic solvent molecules. In a series of data collections, it is demonstrated that small molecules like acetonitrile, methanol and acetone can be removed from the channels by drying without impairing the structure of the hydrogen-bonded peptide host structure. The title compound is one of the very first organic molecules to be found to have this property. Alcohol guests larger than methanol are also absorbed, but they induce a doubling of two axes and a change in the shape and size of the pores. The observed structural modifications explain why these solvent molecules are more or less irreversibly trapped inside the channels.
New phosphate langbeinites, K2
MTi(PO4)3 (M = Er, Yb or Y), and an alternative description of the langbeinite framework
Authors: Norberg Stefan T.
Published: September 2002

Three new potassium rare-earth/titanium phosphate structures, K2ErTi(PO4)3 (KErTP), K2YbTi(PO4)3 (KYbTP) and K2YTi(PO4)3 (KYTP), are presented, all of which are characterized by single-crystal X-ray diffraction studies. In addition, a fourth structure, K2CrTi(PO4)3 (KCrTP), has been reinvestigated. All structures are isostructural to the langbeinite-type structure and result from changes made to the growth constituents in high-temperature flux-growth experiments intended to give structurally modified potassium titanyl phosphate (KTP). The two crystallographically independent octahedra sites (site symmetry 3) have a mixed Ti/M (M = Er, Yb, Y or Cr) population, although the rare-earth metals favour one site while chromium favours the other. An alternative approach for the description of the channels and cation cages in langbeinite and related structures is given using [M
5
X
6O39] units. The framework of langbeinite is compared with that of nasicon using these alternative building units. All of the investigated structures crystallize in space group P213 with Z = 4; a = 10.1053 (2) Å, R = 0.023 (KErTP); a = 10.0939 (8) Å, R = 0.022 (KYbTP); a = 10.1318 (6) Å, R = 0.047 (KYTP); a = 9.8001 (2) Å, R = 0.016 (KCrTP).
Conformational study of S-alkylated isothiosemicarbazones
Authors: Forni Alessandra , Gradinaru Julieta
Published: September 2002

A theoretical investigation of the conformational preferences of S-alkylated isothiosemicarbazones was performed. The structures of such compounds cluster in two groups, according to the different orientation of the —SR group with respect to the hydrazine N atom of the thiosemicarbazide. While the trans arrangement may be more stable for the isolated molecules, owing to N—H...N intramolecular interactions, the cis form is preferred by most compounds in the solid state, as the result of interplay between intra- and intermolecular effects.
Relation between interatomic distances and sizes of ions in molecules and crystals
Authors: Ignatiev Viktor
Published: September 2002

Bond lengths and dissociation energies in alkali halides and alkaline earth oxides and fluorides have been analysed. Ions are considered as static deformable spheres, where an essential part of the electron density is concentrated. In molecules, they are compressed. Moving from molecules to crystals, the bond lengths are extended to such an extent that closed electron shells of ions in alkali halide crystals are separated by distances of ∼20 pm owing to weakened Coulomb attractive forces acting in opposite directions in a crystal. Short-range repulsion is important only within a few surface layers. Some ionic radii are approximately estimated.
Atomic resolution crystal structure of squid ganglion DFPase
Authors: Koepke Juergen , Scharff Eileen I. , Lücke Christian , Rüterjans Heinz , Fritzsch Günter
Published: September 2002

Diisopropylfluorophosphatases (DFP-ases) are capable of detoxifying chemical warfare agents like diisopropylfluorophosphate (DFP) by hydrolysis. The protein reported here was recombinantely expressed in E. coli. The X-ray cystal structure of this enzyme has been refined to a resolution of 0.85 Å and a crystallographic R value of 9.4%. Reversible flash-cooling improved both, mosaicity and resolution of the crystals considerably. The overall structure of this protein represents a six-bladed β-propeller with two calcium ions bound in a central water filled tunnel. 496 water, 2 glycerol, 2 MES-buffer molecules, and 18 PEG fragments of different lengths could be refined in the solvent region. The 208 most reliable residues, without disorder or reduced occupancy in their side-chains, were finally refined without restraints. A subsequent full-matrix refinement cycle for the positional parameters yielded estimated standard deviations (esds) by matrix inversion. The herewith calculated bond lenghts and bond-esds were used to obtain averaged bond lengths, which have been compared to the restraints used in preceding refinement cycles.
Development and characterization of temperature-controlled microreactors for protein crystallization
Authors: Berg Michael , Urban Matthias , Dillner Ulrich , Mühlig Peter , Mayer Günter
Published: September 2002

Physico-chemical properties of the crystallization of biological macromolecules are of particular interest for an efficient way to get high-quality crystals. Concept and realization of a novel temperature-controlled microreactor to study these parameters is revealed. The characterization of the device is focussed on the temperature distribution across the reaction chamber, its long-term stability and accuracy as well as the regeneration of the surface inside the chamber after contamination with a hydrophilic protein (rGFP). We conclude that a microreactor for in situ observation of a temperature-controlled batch crystallization is in place.
Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology
Authors: Malkin A. J. , Plomp M. , McPherson A.
Published: September 2002

Atomic force microscopy (AFM) investigation revealed the sources of disorder and mechanisms of their formation in crystals of an icosahedral plant virus, Cucumber Mosaic Virus (CMV) and structure of the Herpes Simplex Virus (HSV-1). The combination of defects and local disorder in CMV crystals presented here are likely the physical bases for mosaicity in virus crystals, and may be largely responsible for their limited diffraction resolution. High-resolution images of intact, enveloped HSV-1 and the underlying capsid structure demonstrate capabilities of AFM to probe structures of large macromolecular assemblies.
Automated mounting, centering and screening of crystals for high-throughput protein crystallography
Authors: Karain W. I. , Bourenkov G. P. , Blume H. , Bartunik H. D.
Published: September 2002

A fully automated system for screening protein crystals for X-ray diffraction analysis has been designed and is being installed on the beamline BW6 at DORIS in Hamburg, Germany. The system includes robotic mounting of flash-frozen crystals from a storage dewar, centering and alignment of the sample both by optical and X-ray (scattering and fluorescence) techniques, assessment of the diffraction quality of the sample, and SAD/MAD or non-conventional diffraction data acquisition with high-throughput data rates. The system covers all experimental steps required for protein x-ray structure analysis and provides a powerful means for structural genomics projects.
Protein crystallisation on chemically modified mica surfaces
Authors: Falini Giuseppe , Fermani Simona , Conforti Giovanna , Ripamonti Alberto
Published: September 2002

Chemically modified mica sheets have been tested as heterogeneous nucleant surfaces for lysozyme, concanavalin A and thaumatin. Smooth mica surfaces with reduced hydrophilic properties and different density of ionisable groups have been prepared by a silanisation reaction using mixtures of n-propyltriethoxysilane and 3-aminopropyltriethoxysilane in different percentages starting from 0 to 100% of aminosilane. The crystallisation experiments were carried out with the hanging drop vapour diffusion technique. The results suggest that these mica surfaces act as heterogeneous nucleant agents, whose effectiveness is due to non-specific attractive and local interactions between charged residues of the protein and the ionisable groups on the mica surfaces.
Self-interaction chromatography: a novel screening method for rational protein crystallization
Authors: Tessier Peter M. , Vandrey Scott D. , Berger Bryan W. , Pazhianur Rajesh , Sandler Stanley I. , Lenhoff Abraham M.
Published: September 2002

The osmotic second virial coefficient, B
22, has become the quantity most widely used in developing a rational understanding of protein crystallization. In this work a novel method of measuring B22 using self-interaction chromatography (SIC) is presented that is at least an order of magnitude more efficient than traditional characterization methods, such as static light scattering. It is shown that SIC measurements of second virial coefficients for BSA are in quantitative agreement with static light scattering results. The measured virial coefficient for both BSA and myoglobin reveal a surprisingly narrow range of concentrations of ammonium sulfate that promote weakly attractive interactions that are optimal for crystallization. Using the virial coefficient information, myoglobin crystals were obtained by ultracentrifugal crystallization in a rational and rapid manner.
Crystal contacts engineering of aspartyl-tRNA synthetase from Thermus thermophilus: effects on crystallizability
Authors: Charron Christophe , Kern Daniel , Giegé Richard
Published: September 2002

To understand how surface residues in a protein structure influence crystal growth, packing arrangement and crystal quality, crystal surfaces were modified and crystallizability of seven different mutants investigated. The model was aspartyl-tRNA synthetase-1 from Thermus thermophilus, a homodimer (Mr 122,000) with a subunit of 580 amino acids. Engineering concerned modification of amino acids involved in packing contacts in the orthorhombic lattice (P212121) of the synthetase. Comparison of the crystallization behaviour of the mutants indicates a correlation between disruption/addition of packing interactions and crystallizability of the mutants: disruption or modification of lattice contacts prevents crystallization or leads to crystals of poor quality. In contrast, addition of potential contacts leads to well-shaped crystals of same space group and cell parameters than wild-type crystals.
BPTI liquid-liquid phase separation monitored by light and small angle X-ray scattering
Authors: Grouazel S. , Perez J. , Astier J.-P. , Bonneté F. , Veesler S.
Published: September 2002

In the field of protein crystallization, a better knowledge of the nucleation process is essential to control the nucleation rate, the growth and therefore the size and the quality of crystals. With that aim, it becomes clear that the important stage is the determination of the protein phase diagram. We highlighted and investigated the bovine pancreatic trypsin inhibitor (BPTI) binary liquid-liquid phase separation in 350 mM KSCN solutions as a function of temperature. We measured the low concentration part of the binodal curve using light scattering and optical microscopy. We show, from small angle X-ray scattering experiments, that the high concentrated phase sediments in the bottom of the capillary and we analysed the low concentrated phase in terms of monomers/decamers equilibrium.
Protein L mutants for the crystallization of antibody fragments
Authors: Stura Enrico A. , Graille Marc , Housden Nicholas G. , Gore Michael G.
Published: September 2002

In many cases, antibody and their complexes can be crystallized and their structure determined without major difficulties. The remaining problematic cases may be approached through techniques such as of combinatorial complex crystallization which uses immunoglobulin binding proteins (IBP). The range of lattices that can be made using this method can be expanded by engineering mutants of IBP domains. We have designed Peptostreptococcus magnus protein L (PpL) mutants with altered immunoglobulin light chain binding characteristics. While the wild type PpL has two binding sites, some of the mutants contact the light chain via only one site. Other mutants have combinations of weakened first and second binding sites that modify their crystallization properties and their packing mode. In this study, we have selected PpL mutants with different behavior and that are most useful for crystallization and we present the various packing modes obtained so far.
Heparin-aggregated RANTES can be crystallised
Authors: Stura Enrico A. , Martin Loïc , Lortat-Jacob Hugues , Vivès Romain , Vita Claudio
Published: September 2002

Crystals of RANTES (regulated on activation normal T-cell expressed) have been grown in the presence of heparin-derived sulphated oligosaccharides which cause RANTES to aggregate severely. The crystals have a tendency to be polycrystalline but diffract to 3.8 - 1.8 Å resolution. Oligosaccharides length and stoichiometry influence aggregation, nucleation and crystal growth and quality. Surprising, rather than inhibiting crystallisation, aggregation appears to stimulate nucleation. We have co-crystallised RANTES in the presence of oligosaccharides ranging in size from 1 to 12 sugar moieties. The best crystals, both according to size and diffraction quality have been obtained with a six moiety sugar. Crystals grow in the same space group with similar cell parameters as previously reported. We find no homogeneous binding of the sulphated sugars to RANTES even after eliminating sulphate from the crystallisation conditions to avoid competition with sulphates from the sulphated sugars. There is no electron density at the sulphate positions characterised in the original structure and the residues involved in sulphate binding adopt a different side chain orientation. Either heterogeneous binding of the sulphated sugars or an active ratchet-like mechanism by which the sulphated sugars are eliminated from the crystal lattice as the crystals grow may be responsible for the absence of sugars in the structure. The fact that aggregated proteins can be crystallised is important, since it is generally accepted that proteins that are polydisperse by light dynamic scattering are poor candidates for crystallisation trials.
Scaffolds for protein crystallisation
Authors: Stura Enrico A. , Taussig Michael J. , Sutton Brian J. , Duquerroy Stéphane , Bressanelli Stéphane , Minson Anthony C. , Rey Felix A.
Published: September 2002

In the absence of a method to ensure that crystals can be obtained for any given protein, the possibility of developing scaffolds for protein crystallisation becomes attractive. Among several approaches that could yield scaffolds, two are particularly promising: the first is based on immunoglobulin Fab fragments and immunoglobulin binding proteins while the second is based on fusion proteins. In the Fab based scaffold, the protein of interest is the antigen recognised by the antibody. In the second case, it is a protein fused to one of the scaffold components. The operational difference between the two methods is the existence of a flexible covalent tether compared to a highly specific interaction. The relative merits and disadvantages of each approach are discussed here. We also describe a lattice obtained through a combinatorial approach which appears to have the required properties to be considered a scaffold. The system makes use of an Fab derived from a rheumatoid factor and an Fc-fusion protein. The Fc-fusion system is ideal for enhanced expression of glycoproteins in mammalian cells and provides a useful tag for their purification. The molecular replacement shows a mode of binding for this rheumatoid factor that is not competitive with bacterial Fc-binding proteins. Hence it may be possible to generalise the method to include bacterial expression of fusion proteins with either protein A or protein G as the fusion partner.
Disulphide dimerised peptide creates a crystal contact in an anti-peptide antibody
Authors: Stura Enrico A. , Tête-Favier Frédérique , Muller Sylviane , Aubry André
Published: September 2002

Although many Fab derived from human and murine antibodies have been crystallised, several such fragments, including anti-peptide Fab 4x11, remain problematic for crystallisation. Diffracting crystals have been obtained for this Fab only in complex with a cysteine containing peptide CGGIRGERA. The IRGERA portion contained in the C-terminus of histone H3 is recognised by the monoclonal antibody and the CGG portion is an essential spacer. Crystallisation experiments and seeding studies show that disulphide bond formation is essential for obtaining crystals. Data has been collected to 2.7 Å resolution, and the structure solved by molecular replacement. The asymmetric unit contains two antibodies whose binding sites are face-to-face in an non-crystallographic approximate two-fold rotational axis. We find two Fab in the asymmetric unit with the two antigen combining sites facing each other. This result was unexpected since it has been common practice to avoid the cysteine-containing peptides because of heterogeneity, since the peptide solution is likely to contain both dimeric and monomeric peptides. This result suggests that the cysteine containing peptides used in immunisation for coupling them to a carrier protein could also be used to screen for crystals. Structural data obtained for the same peptides as those used in the immunisation is valuable to evaluate to what extent the linker to the carrier protein may have contributed to the shaping of the antibody binding site. The introduction of exposed cysteines on the surface of proteins by site directed mutagenesis could help resolve difficult crystallisation cases. Should these not form a disulphide bridge in the crystal but nonetheless crystallise, the free cysteine could be used to make a heavy atom derivative for isomorphous replacement.
Crystallization of HLA-DR4 fused to an immunodominant collagen II peptide implicated in rheumatoid arthritis
Authors: Hurlbert Jason , Izard Tina
Published: September 2002

Major histocompatibility complex (MHC) class II molecules are key players in antigen-specific CD4+ T cell stimulation, despite their lack of discrimination between "self" and foreign antigens. The susceptibility of many individuals to autoimmune diseases is directly attributed to this lack of specificity, as well as to the expression of subclasses of MHC class II molecules. Increased susceptibility to the autoimmune disease rheumatoid arthritis (RA) has been attributed to the expression of the MHC class II alleles HLA-DR1 and HLA-DR4. To define the structural requirements of the HLA-DR4 protein in the autoimmune response of RA, we have crystallized HLA-DR4 with the immunodominant peptide from human collagen II, covalently linked to the N-terminus of the β-chain [HLA-DR4/hCII(257-273)]. Crystallization time, crystal size, and reproducibility were greatly improved by macroseeding into microdialysis buttons.
Nucleation of protein crystals in a wide continuous supersaturation gradient
Authors: Penkova A. , Chayen N. , Saridakis E. , Nanev Chr. N.
Published: September 2002

By using a supersaturation gradient along a protein solution contained in a glass capillary tube, we modified the classical double pulse technique, thus substantially accelerating the procedure of measurement of nucleation parameters. Data for the number of crystal nuclei, n
vs nucleation time, t, were obtained for hen-egg-white lysozyme, chosen as a model because of the availability of reliable solubility data in the literature. The stationary nucleation rate and the nucleation time lag have been measured. Quantitative data for the work required for nucleus formation (Ak
= 4.3x10-13 erg) and the size of the critical cluster (three molecules) were also obtained. Besides, it was observed that Ostwald ripening seems to play an important role for nucleation times longer than 150 min. Using the same technique, semi-quantitative investigations were performed with porcine pancreatic trypsin.
Charge separation induces conformational changes in the photosynthetic reaction centre of purple bacteria
Authors: Fritzsch Günter , Koepke Jürgen , Diem Ralf , Kuglstatter Andreas , Baciou Laura
Published: September 2002

X-ray structures of the wild-type reaction centre from Rhodobacter
sphaeroides have been determined to a resolution of 1.87 Å in the neutral (dark) state and to 2.06 Å in the charge-separated (light-excited) state. Whereas the overall protein structures of both states are rather similar, the domain around the secondary quinone shows significant shifts. The quinone molecule itself is observed at two different positions. In the neutral state, 55% of the quinone is located distally and 45% proximally to the cytoplasmic side. After excitation by light, however, at least 90% of the quinone is found at the proximal position. Results presented by Stowell et al. (1997) are confirmed, but the quality of crystallographic data has been improved. We compare the data with the structure of the mutant RC L209 PY that keeps the QB molecule in the proximal position even in the charge-neutral state.
Application of the effects of ionic strength reducing agents in the purification and crystallization of chitinase A
Authors: Papanikolau Yannis , Petratos Kyriacos
Published: September 2002

The effects of ionic strength reducing agents may find a large number of applications. Based on these effects, we have redesigned the purification scheme of Chitinase A (ChiA) from Serratia
marcescen. This scheme led to reproducibly crystallizable enzyme in both salting-in and salting-out conditions, which are presented here. Herein, we demonstrate some experimental applications of the ionic strength reducing agents theory and, in parallel, provide further evidence of the theory's correctness. Finally, we report a new crystal form produced recently in salting-in crystallization experiments. This form may allow the co-crystallization of ChiA mutants with longer substrates.
Vapor diffusion, nucleation rates and the reservoir to crystallization volume ratio
Authors: Forsythe Elizabeth L. , Maxwell Daniel L. , Pusey Marc
Published: September 2002

In a classical vapor diffusion crystallization, the protein solution is mixed in a 1:1 ratio with the reservoir solution, containing one or more precipitant species, after which the two are placed in an enclosed chamber. As the vapor pressure is lower for the reservoir solution, due to its higher solute concentration, there is a net transfer of water through the vapor phase from the protein droplet to the reservoir. In theory, the initial conditions in the droplet are such that the protein is in either a metastable or undersaturated state with respect to crystal nucleation. The loss of water serves to both concentrate the protein and the precipitant concentrations within the drop, bringing the protein past the metastable point to nucleation. The equilibration rate is a function of the precipitant(s) used, their concentration, the temperature, the distance between the two surfaces, and the droplet to reservoir volume ratio. For a given reservoir volume smaller droplets equilibrate faster, the rate being inversely linear with the droplet volume. In attempts to maximize the number of crystallization trials, and as crystals in the 100 – 200 μm size range are sufficient, it has currently become standard practice to use starting droplet volumes of 2 - 4 μl, with reservoir volumes typically in the 200 to 500 μl range. The equilibration rates are maximized, and for most common salt concentrations and higher concentrations of polyethylene glycol (PEG) and 2-methyl-2,4-pentanediol (MPD) one can reasonably estimate that equilibration has occurred within 3 to 6 days at room temperature. Crystals appearing after this time are essentially grown under batch conditions. We experimentally find that altering the reservoir to droplet volume ratio, by changing the reservoir volume, from 50:1 (high ratio) to 5:1 (low ratio), on average increases the equilibration time by approximately 50 % when tested with solutions of 50% MPD, 1.5 M NaCl, or 30 % PEG400. However, experiments with two proteins, chicken egg white lysozyme and concanavalin a, showed an unexpected trend of slightly faster nucleation and larger crystals in the lowest ratio experiments.
From conventional crystallization to better crystals from space: a review on pilot crystallogenesis studies with aspartyl-tRNA synthetases
Authors: Lorber B. , Théobald-Dietrich A. , Charron C. , Sauter C. , Ng J. D. , Zhu D.-W. , Giegé R.
Published: September 2002

Aspartyl-tRNA synthetases were the model proteins in pilot crystallogenesis experiments. They are homodimeric enzymes of Mr~125 kDa that possess as substrates a transfer RNA, ATP and aspartate. They have been isolated from different sources and were crystallized either as free proteins or in association with their ligands. This review discusses their crystallisability with emphasis to crystal quality and structure determination. Crystallization in low diffusivity gelled media or in microgravity environments is highlighted. It has contributed to prepare high-resolution diffracting crystals with better internal order as reflected by their mosaicity. With AspRS from Thermus thermophilus, the better crystalline quality of the space-grown crystals within APCF is correlated with higher quality of the derived electron density maps. Usefulness for structural biology of targeted methods aimed to improve the intrinsic physical quality of protein crystals is highlighted.
Crystallization of RNA/protein complexes
Authors: Garber Maria , Gongadze George , Meshcheryakov Vladimir , Nikonov Oleg , Nikulin Alexey , Perederina Anna , Piendl Wolfgang , Serganov Alexander , Tishchenko Svetlana
Published: September 2002

Different complexes of ribosomal proteins with specific rRNA fragments have been crystallized and studied by our group during the last six years. There are several factors important for successful crystallization of RNA/protein complexes, among them: length and content of RNA fragments, homogeneity of RNA and protein preparations, stability of the complexes, conditions for mixing RNA and protein components before crystallization, effect of Se-Met on RNA/protein complex crystal quality. In this paper we describe findings and methodical details, which helped us to succeed in obtaining X-ray quality crystals of several RNA/protein complexes.
Crystallization of the collagen-like polypeptide (PPG)10 aboard the International Space Station. 1. Video observation
Authors: Vergara Alessandro , Corvino Ermanno , Sorrentino Giosué , Piccolo Chiara , Tortora Alessandra , Carotenuto Luigi , Mazzarella Lelio , Zagari Adriana
Published: September 2002

Single chains of the collagen model polypeptide with sequence (Pro-Pro-Gly)10, hereafter referred to as (PPG)10, aggregate to form rod-shaped triple helices. Crystals of (PPG)10 were grown in the Advanced Protein Crystallization Facility (APCF) both onboard the International Space Station (ISS) and on Earth. The experiments allow the direct comparison of four different crystallization environments for the first time: solution in microgravity (μg), agarose gel in μg, solution on earth, and gel on earth. Both on board and on ground, the crystal growth was monitored by a CCD video camera. The image analysis provided information on the spatial distribution of the crystals, their movement and their growth rate. The analysis of the distribution of crystals reveals that the crystallization process occurs as it does in batch conditions. Slow motions have been observed onboard the ISS. Different to Space-Shuttle experiment, the crystals onboard the ISS moved coherently and followed parallel trajectories. Growth rate and induction time are very similar both in gel and in solution, suggesting that the crystal growth rate is controlled by the kinetics at the interface under the used experimental conditions. These results provide the first data in the crystallogenesis of (PPG)10, which is a representative member of non-globular, rod-like proteins.
Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 Å resolution
Authors: Krauspenhaar R. , Rypniewski W. , Kalkura N. , Moore K. , DeLucas L. , Stoeva St. , Mikhailov A. , Voelter W. , Betzel Ch.
Published: September 2002

The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album in complex with adenine has been refined to 1.9 Å resolution. High quality crystals of the ML-I complex were obtained by the method of vapour diffusion using the high density protein crystal growth system (HDPCG) on the international space station, mission ISS 6A. Hexagonal crystals were grown during three months under microgravity conditions. Diffraction data to 1.9Å were collected applying synchrotron radiation and cryo- techniques. The structure was refined subsequently to analyse the structure of ML-I and particularly the active site conformation, complexed by adenine that mimics the RNA substrate binding.
The TB structural genomics consortium crystallization facility: towards automation from protein to electron density
Authors: Rupp Bernhard , Segelke Brent W. , Krupka Heike I. , Lekin Tim , Schäfer Johana , Zemla Adam , Toppani Dominique , Snell Gyorgy , Earnest Thomas
Published: September 2002

The crystallization facility of the TB (Tuberculosis) structural genomics consortium, one of nine NIH sponsored P50 structural genomic centres, provides TB consortium members with automated crystallization, data collection and basic molecular replacement (MR) structure solution up to bias minimized electron density maps. Crystallization setup of up to ten proteins per day follows the CRYSTOOL combinatorial screen protocol using a modular and affordable robotic design with an open architecture. Components include screen preparation, plate setup, automated image acquisition and analysis, and optimisation design. A new 96 well crystallization plate has been designed for optimal robotic handling while maintaining ease of manual crystal harvesting. Robotic crystal mounting, screening, and data collection are conducted in-house and at the Advanced Light Source (ALS) in Berkeley. A simple automated protocol based on MR and homology based structure prediction automatically solves modestly difficult problems. Multiple search models are evaluated in parallel MR and the best multi-segment rigid body refined MR solution is subjected to simulated annealing torsion angle molecular dynamics using CNS, bringing even marginal MR solutions within the convergence radius of the subsequent highly effective bias removal and map reconstruction protocol, Shake&wARP, used to generate electron density for initial rebuilding. Real space correlation plots allow rapid assessment of local structure quality. Modular design of robotics and automated scripts using publicly available programs for structure solution allow for efficient high throughput crystallography - at a reasonable cost.
Phase homogeneity and crystal morphology of the malaria pigment β-hematin
Authors: Bohle D. Scott , Kosar Andrew D. , Stephens Peter W.
Published: September 2002

Hemoglobin digestion in the intraerythrocytic trophozoite stages of the malaria parasite releases large quantities of heme, which is then detoxified by crystallization into regular crystallites, which are subsequently secreted into the host vascular network as malaria pigment. This crystalline product is isostructural with the synthetic phase b-hematin, and its structure, solved from its powder diffraction pattern, (Pagola et al., 2000), corresponds to a hydrogen bonded chain of propionate linked dimers, Figure 1. This is an example where the crystalline phase is the macromolecule of direct biological interest, particularly in light of the currently accepted hypothesis for the quinoline antimalarial drug action being the inhibition of b-hematin formation and biosynthesis. A surprisingly array of spectroscopically similar closely related phases can also form during the reactions which are used to synthesize b-hematin. Scanning electron microscopy and X-ray powder diffraction have been used to characterize these materials. Taken together these results indicate that infrared spectroscopy, in itself, is insufficient to identify synthetic analogs to malaria pigment and that a combination of electronmicroscopy and powder diffraction are required to unambiguously characterize these heme aggregates.
Time-resolved scattering investigations of brome mosaic virus microcrystals appearance
Authors: Casselyn M. , Finet S. , Tardieu A. , Delacroix H.
Published: September 2002

The behavior of brome mosaic virus in solution as a function of physico-chemical conditions has already been characterized by Small Angle X-ray Scattering studies. The most striking result was that the precipitates induced by the addition of polyethylene glycol were in fact made of microcrystals. This result was reinvestigated on the ID2 beamline at ESRF (Grenoble, France) to determine whether there was an amorphous state before the organized one, and measure the necessary period of latency for the microcrystals to form. The stopped-flow device associated to the high brilliance of the beamline enabled us to characterize the growth of the diffraction peaks as a function of time.
Solvent entropy contribution to the free energy of protein crystallization
Authors: Vekilov Peter G. , Feeling-Taylor Angela R. , Yau Siu-Tung , Petsev Dimiter
Published: September 2002

We show with three proteins that trapping and release of the water molecules upon crystallization is a determinant of the crystallization thermodynamics. With HbC, a strong retrograde solubility dependence on temperature yields a high positive enthalpy of 155 kJ mol-1, i.e., crystallization is only possible because of the huge entropy gain of 610 J mol-1K-1, stemming from the release of up to 10 water molecules per protein intermolecular contact. With apoferritin, the enthalpy of crystallization is close to zero. The main component in the crystallization driving force is the entropy gain due to the release upon crystallization of two water molecules bound to one protein molecules in solution. With both proteins, the density of the growth sites imaged by AFM is in excellent agreement with a calculation using the crystallization free energy. With lysozyme, the entropy effect due to the restructuring of the water molecules is negative. This leads to higher solubility.
Bacillus subtilis division protein DivIVA – screen for stable oligomer state conditions
Authors: Muchová Katarína , Kutejová Eva , Pribišová Ludmila , Wilkinson Anthony J. , Barák Imrich
Published: September 2002

The cell division protein DivIVA is predicted to be a coiled-coil, tropomyosin–like protein, that self-associates both in vivo and in vitro into oligomers of up to 10-12 monomers. A simple and quick screen for conditions supporting the stable oligomer structure has been developed revealing that DivIVA forms a homogeneous oligomer in the presence of PEGs (PEG 4K or PEG 8K and PEG 1K).
Separating nucleation and growth in protein crystallization using dynamic light scattering
Authors: Saridakis Emmanuel , Dierks Karsten , Moreno Abel , Dieckmann Matthias W. M. , Chayen Naomi E.
Published: September 2002

A means of controlling crystallization is to separate the phases of nucleation and growth. Methods to achieve this, other than seeding, involve lowering the supersaturation by changing the temperature or diluting drops after incubating them for a given time at nucleation conditions. However, by the time nuclei or crystals are visible under the microscope too many nuclei will have formed. Dynamic Light Scattering was applied practically, to determine the most likely time for nucleation-growth decoupling to be performed successfully. The time at which DLS showed a significant change in the size-distribution of species in solution, corresponded to that optimal time.
Analysis of the influence of coupled diffusion on transport in protein crystal growth for different gravity levels
Authors: Castagnolo D. , Vergara A. , Paduano L. , Sartorio R. , Annunziata O.
Published: September 2002

Diffusion has a central role in protein crystal growth both in microgravity conditions and on ground. Recently several reports have been focused on the importance to use the generalized Fick's equations in n-component systems where crystals grow. In these equations the total flux of each component is produced by the own concentration gradient (main flow) and by the concentration gradient of the other components (cross-flow) present in the system. However in literature the latter effect is often neglected, and the so-called pseudo-binary approximation is used. Lin et al. (1995) proposed a mathematical model to evaluate the concentration profile of the species present around a growing protein crystal. Although the model is reliable, it suffers of the pseudo-binary approximation (neglecting cross term diffusion coefficients and using binary diffusion coefficients), probably because of the lack of multicomponent diffusion data. The present model is based on the experimental set-up proposed by Lin et al. (1995). Nevertheless we have included the coupled diffusion effects, according to the correct description of the matter transport through the generalized Fick's equations. The crystal growth rate is calculated for different gravity levels. The model has been applied to the ternary lysozyme-NaCl-water and quaternary lysozyme-poly(ethylene glycol) (PEG)-NaCl-water systems using recent diffusion data.