bluuebunny/crossref_metadata_2025 huggingface dataset:
Structures and phase transitions of the A
7PSe6 (A = Ag, Cu) argyrodite-type ionic conductors. II. β- and γ-Cu7PSe6
Authors: Gaudin E. , Boucher F. , Petricek V. , Taulelle F. , Evain M.
Published: July 2002

The crystal structures of two of the three polymorphic forms of the Cu7PSe6 argyrodite compound are determined by means of single-crystal X-ray diffraction. In the high-temperature form, at 353 K, i.e. 33 K above the first phase transition, γ-Cu7PSe6 crystallizes in cubic symmetry, space group F4¯3m. The full-matrix least-squares refinement of the structure leads to the residual factors R  = 0.0201 and wR = 0.0245 for 31 parameters and 300 observed independent reflections. In the intermediate form, at room temperature, β-Cu7PSe6 crystallizes again in cubic symmetry, but with space group P213. Taking into account a merohedric twinning, the refinement of the β-Cu7PSe6 structure leads to the residual factors R  = 0.0297 and wR  = 0.0317 for 70 parameters and 874 observed, independent reflections. The combination of a Gram–Charlier development of the Debye–Waller factor and a split model for copper cations reveals the possible diffusion paths of the d
10 species in the γ-Cu7PSe6 ionic conducting phase. The partial ordering of the Cu+
d
10element at the phase transition is found in concordance with the highest probability density sites of the high-temperature phase diffusion paths. A comparison between the two Cu7PSe6 and Ag7PSe6 analogues is carried out, stressing the different mobility of Cu+ and Ag+ and their relative stability in low-coordination chalcogenide environments.
Absolute measurement of structure factors using a new dynamical interference effect
Authors: Hart M. , Milne A. D.
Published: July 2002

A new method of determining X-ray scattering factors by dynamical interference is described. The theoretical background to the interference effect is discussed in detail and an expression for relating the fringe period to the structure factor is developed. The method relies on anomalous transmission and is therefore most suitable for measurements on nearly perfect crystals of high atomic weight. It also has the attractive property of being insensitive to slowly varying lattice strains. Applying the method to the 220 reflexion of silicon a value of 8.487 ± 0.017 for the atomic scattering factor has been obtained using Mo Kα
1 radiation. This value is in excellent agreement with the author's previous results using the Pendellösung method.
The temperature factor of an atom in a rigid vibrating molecule. I. Isotropic thermal motion
Authors: Willis B. T. M. , Pawley G. S.
Published: July 2002

The temperature factor of an atom in a molecular crystal has been derived in terms of the rigid-body parameters (u
2) and (ω2), where (u
2) is the mean-square amplitude of translational displacement of the molecule in any direction and (ω
2) is the mean-square amplitude of angular (librational) displacement about any axis through the centre of inertia of the molecule. The analysis, which is appropriate to a cubic crystal containing rigid molecules undergoing isotropic thermal motion, is correct to the second power of (ω
2); the second-order treatment is necessary for interpreting accurate Bragg intensity data such as those discussed in a subsequent paper. Substitution of the temperature factor into the structure-factor equation yields an expression containing terms which can be identified with the first, second and third cumulants of the `cumulant expansion' model of thermal motion.
Short-range order in ND4Br studied by diffuse neutron scattering
Authors: Seymour R. S.
Published: July 2002

Diffuse elastic scattering of neutrons has been observed from a single crystal of deuterated ammonium bromide and is interpreted as being due to short-range order among ammonium ion orientations. Both the temperature dependence of the diffuse intensity and its distribution in reciprocal space can be described in terms of a simple Ising model of the order-disorder transition. An expression for the diffuse intensity obtained from the mean-field approximation to the Ising model is least-squares fitted to the data. Interactions between first, second and third nearest neighbour ammonium ions have to be included in the model to give an adequate fit. The interaction energies so obtained are compared with calculations based on a simple electrostatic theory, For agreement, a charge of 0.358e on hydrogen atoms and a polarizability of 1.40 Å3 for Br− ions have to be assumed in the calculations and the significance of these unlikely values is discussed.
An unconventional view of the `closest sphere packings'
Authors: Brunner G. O.
Published: July 2002

If it is made a condition that the volume of the arrangement be finite, the close sphere packings may be regarded as arrangements of objects having the largest possible separations between neighbours. In this case the arrangement of the centres is considered, and the assumptions of a spherical shape and of mutual contact are not necessary. The motives for applying this viewpoint in crystal chemistry, and its fruitfulness, are discussed. The paper aims at a plausible understanding of crystal structures and their metrics.
Structural studies by high-resolution electron microscopy: intergrowth of ReO3 and tetragonal tungsten bronze-type structures in the system Nb2O5–WO3
Authors: Iijama S.
Published: July 2002

With high-resolution electron microscopy new crystal structures were found in the binary system of Nb2O5WO3 oxides. The compounds are proposed to have the mole ratios 4Nb2O5. 22WO3 and 4Nb2O5. 50WO3. The crystal structures are ascribed to intimate intergrowths of two known structures, the ReO3 type and tetragonal tungsten bronze type. The latter grows coherently in the host lattice of the former, forming regularly arranged slabs. The coherent intergrowth of the tetragonal tungsten bronze structures is described as the 'rotation operation' on the ReO3-type structure.
A simple method for obtaining triclinic cell parameters from Weissenberg photographs from one crystal setting
Authors: Hebert H.
Published: July 2002

A simple method is described for the interpretation of Weissenberg photographs and the determination of triclinic cell parameters from a single setting of the crystal. The theoretical approach is followed by an example illustrating the procedure. A comparison of these results with those derived from diffractometer measurements is made.
The effect of bonding electrons on molecular dimensions as determined by X-rays
Authors: Pant L. M.
Published: July 2002

The central-bond shortening in disubstituted benzenes having an electron-withdrawing group and an electron-releasing group in para positions is well known. However, even in several disubstituted benzenes having electron-withdrawing groups in both para positions, X-ray analysis shows a central-bond shortening. In monosubstituted benzenes, the middle bonds and the bonds farthest from the substituent show bond shortenings which cannot be accounted for by librational motion alone, it is pointed out that these apparent shortenings are caused by the asymmetry of the charge distribution around the C atoms bonded to the H atoms. This charge asymmetry is to a large extent an artifact of the refinement procedure.
Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kα wavelength
Authors: Yang Cheng , Pflugrath J. W.
Published: July 2002

The anomalous signal of S atoms is easily detected at the Cu Kα wavelength of a non-synchrotron source with current data-collection methods. The position of sulfur and other anomalous scatterers can be located through an anomalous difference Fourier map (F
+ − F
−, φcalc − 90°). It has been discovered experimentally that even low-quality preliminary phases are often sufficient to find anomalous scatterers. Their anomalous signal in the native crystal can contribute to significant improvement in phase refinement. This technique has been applied to solve the crystal structures of orthorhombic lysozyme and thaumatin. Furthermore, the structure of trypsin was solved using only the diffraction data set from a native crystal collected at a single wavelength (Cu Kα) from a rotating-anode X-ray generator. The anomalous scattering of sulfur was essential to solve the structure of trypsin which was initially phased from a single intrinsic Ca2+ atom. The positions of the S atoms of lysozyme and thaumatin were found using the initial SIRAS phases and used in phase refinement. The overall figures of merit and those in each resolution shell were consistently improved. This resulted in much improved electron-density maps even when the diffraction data were limited to 2.5 Å resolution or worse. Furthermore, peaks from S atoms and other anomalous scatterers in anomalous difference Fourier maps can confirm the tracing of the peptide chain and also provide independent unbiased confirmation of molecular-replacement results. Thus, the anomalous signal of S atoms can contribute to many aspects of solving protein structures and should be used routinely.
Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template
Authors: Mittl Peer R. E. , Chène Patrick , Grütter Markus G.
Published: July 2002

The molecular replacement method is a powerful technique for crystal structure solution but the use of NMR structures as templates often causes problems. In this work the NMR structure of the p53 tetramerization domain has been used to solve the crystal structure by molecular replacement. Since the rotation- and translation-functions were not sufficiently clear, additional information about the symmetry of the crystal and the protein complex was used to identify correct solutions. The three-dimensional structure of residues 326–356 was subsequently refined to a final R factor of 19.1% at 1.5 Å resolution.
Structure of a Monoclinic Crystal Form of Cytochrome b1 (Bacterioferritin) from E. coli
Authors: Dautant Alain , Meyer Jean-Brice , Yariv Joseph , Précigoux Gilles , Sweet Robert M. , Kalb A. Joseph , Frolow Felix
Published: July 2002

Crystals of E. coli cytochrome b1, alias bacterioferritin, were grown from a low ionic strength solution. The resulting monoclinic P21 structure was solved by molecular replacement and refined using noncrystallographic symmetries applied to the fundamental unit, consisting of two protein subunits and a single haem. From the Patterson self-rotation results it was shown that the asymmetric unit of the monoclinic crystal consists of 12 such dimers and corresponds to a complete, nearly spherical, molecule of bacterioferritin (Mr
 = 450 kDa) of 432 point-group symmetry. It is thus the most symmetrical cytochrome. As previously determined for the tetragonal form, the haem is located in a special position on a local twofold axis of the dimer. A bimetal centre is also observed within the four-helix bundle of each monomer; a metal-binding site is located on the fourfold axis.
Crystallization and preliminary X-ray analysis of tyrosine aminotransferase from Trypanosoma cruzi epimastigotes
Authors: Nowicki Cristina , Montemartini Marisa , Hunter Giselle Reynoso , Blankenfeldt Wulf , Kalisz Henryk M. , Hecht Hans-Jürgen
Published: July 2002

Tyrosine aminotransferase from Trypanosoma cruzi has been crystallized from PEG 4000 at pH 6.8. The crystals belong to the monoclinic space group P21 and have lattice constants of a = 59.1, b = 103.0, c = 77.8 Å, β = 113.1° for a data set measured at 138 K. The presence of a non-crystallographic twofold axis together with a Matthews parameter Vm
of 2.5 Å3 Da−1 indicates that the asymmetric unit contains one dimeric molecule. The crystals diffract to at least 2.7 Å and are stable in the X-ray beam in a shock-frozen state. Native data sets have been collected at temperatures of 285 and 138 K using a Siemens X1000 detector on a rotating-anode generator.
Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus
Authors: Kumagai Takanori , Muta Kengo , Matoba Yasuyuki , Kawano Yoshiaki , Kamiya Nobuo , Davies Julian , Sugiyama Masanori
Published: July 2002

A bleomycin-binding protein (BLMA) produced by bleomycin-producing Streptomyces verticullus was crystallized in a form suitable for X-ray diffraction analysis using the vapor-diffusion method. Crystals were grown at pH 5.7, in 0.2 M NH4 actate and 0.1 M Na acetate, using 30% PEG 4000 as a precipitant. They belong to the orthorhombic system, with space group P21212, cell dimensions a = 54.90, b = 67.94, c = 35.60 Å, and one BLMA molecule in the asymmetric unit. The crystals diffract X-rays well and the diffraction intensity data was collected up to 1.5 Å resolution with a merging R value of 0.054 at beamline 6B of the Photon Factory. The diffraction data set is 94% complete.
Expression, purification and crystallization of the catalytic subunit of protein kinase CK2 from Zea mays
Authors: Guerra Barbara , Niefind Karsten , Pinna Lorenzo A. , Schomburg Dietmar , Issinger Olaf-Georg
Published: July 2002

The catalytic (α) subunit of protein kinase CK2 (CK2α) was originally cloned and overexpressed in the Escherichia coli strain pT7-7/BL21(DE3). The protein has been purified to homogeneity and crystallized. The crystals belong to the monoclinic space group C2, they have unit-cell parameters a = 142.6, b = 61.3, c = 45.6 Å, β = 103.3° and diffract X-rays to at least 2.0 Å resolution. The calculated crystal packing parameter is Vm
= 2.47 Å3 Da−1 suggesting that one CK2α molecule is contained in the asymmetric unit and that the solvent content of the unit cell is 50%.
Crystallization and preliminary crystallographic analyses of pokeweed antiviral protein from seeds
Authors: Li Hong-Min , Zeng Zong-Hao , Hu Zhong , Wang Da-Cheng
Published: July 2002

Pokeweed antiviral protein from seeds (PAP-S) is a ribosome inactivating protein which has lowest toxicity and highest inhibition activity as opposed to other pokeweed antiviral proteins and its three potential glycosylation sites (10, 44, 255) were shown to bind to N-acetylglucosamine. Good quality crystals of PAP-S were grown at high protein concentration (100 mg ml−1) and high temperature (306 K). The crystals have space group I222 and cell parameters a = 78.7, b = 85.2 and c = 93.0 Å. An X-ray diffraction data set with resolution up to 1.8 Å was collected. This high-resolution data will help to locate the sugars bound to the protein and provide accurate structural data for understanding structure–function relationships of PAP-S.
Expression, crystallization and preliminary X-ray analysis of ligand-free human glutathione S-transferase M2–2
Authors: Patskovska Larysa N. , Fedorov Alexander A. , Patskovsky Yury V. , Almo Steven C. , Listowsky Irving
Published: July 2002

Human glutathione-S-transferase M2–2 (hGSTM2–2) was expressed in Escherichia coli and purified by GSH-affinity chromatography. The recombinant enzyme and the protein isolated from human tissue were indistinguishable based on physicochemical, enzymatic and immunological criteria. The catalytically active dimeric hGSTM2–2 was crystallized without GSH or other active-site ligands in two crystal forms. Diffraction from form A crystals extends to 2.5 Å and is consistent with the space group P21 (a = 53.9, b = 81.5, c = 55.6 Å, β = 109.26 Å) with two monomers in the asymmetric unit. Diffraction from form B crystals extends to 3 Å and is consistent with a space group P212121 (a = 57.2, b = 80.7, c = 225.9 Å) with two dimers in the asymmetric unit. This is the first report of ligand-free mu-class GST crystals, and a comparison with liganded complexes will provide insight into the structural consequences of substrate binding which are thought to be important for catalysis.
Crystallization and preliminary X-ray diffraction studies of homoserine dehydrogenase from Saccharomyces cerevisiae
Authors: DeLaBarre Byron , Jacques Suzanne L. , Pratt Catharine E. , Ruth Derek A. , Wright Gerard D. , Berghuis Albert M.
Published: July 2002

Recombinant homoserine dehydrogenase from Saccharomyces cerevisiae has been crystallized in three different forms. Crystals of the apo-enzyme belong to the tetragonal space group P4 and have unit-cell-dimensions a = b = 130 and c = 240 Å. The resolution limit for these crystals is 3.9 Å. Crystals of homoserine dehydrogenase grown in the presence of the co-factor NAD+ have the tetragonal space group P41212 or its enantiomorph P43212. The unit-cell dimensions for these crystals are a
= b = 80.4 and c = 250.2 Å, and the observed resolution limit is 2.2 Å. Protein crystals grown in the presence of the product L-homoserine and the inert NAD+ analogue 3-aminopyridine adenine dinucleotide belong to the monoclinic space group P21 with unit-cell parameters a = 58.8, b = 104.2, c = 120.7 Å, β = 91.9°. This last crystal form has a diffraction limit of 2.7 Å resolution.
Protein Crystal Growth in the Advanced Protein Crystallization Facility on the LMS Mission: a Comparison of Sulfolobus solfataricus Alcohol Dehydrogenase Crystals Grown on the Ground and in Microgravity
Authors: Esposito L. , Sica F. , Sorrentino G. , Berisio R. , Carotenuto L. , Giordano A. , Raia C. A. , Rossi M. , Lamzin V. S. , Wilson K. S. , Zagari A.
Published: July 2002

Crystals of alcohol dehydrogenase from Sulfolobus solfataricus were grown in the Advanced Protein Crystallization Facility during the Life and Microgravity Sciences Spacelab mission on the US Space Shuttle. Large diffracting crystals were obtained by dialysis, whereas only poor-quality crystals were obtained by vapour diffusion. The quality of both the microgravity and ground-based crystals was analysed by X-ray diffraction. There was some improvement in terms of size and diffraction resolution limit for the microgravity crystals. However, the twinning observed in the Earth-grown crystals was also present for those grown in microgravity.
Expression, purification, crystallization and preliminary X-ray diffraction analysis of human uroporphyrinogen decarboxylase
Authors: Laterrière Martine , Langlois d'Estaintot Béatrice , Dautant Alain , Précigoux Gilles , Hombrados Isabelle , de Verneuil Hubert
Published: July 2002

A recombinant human uroporphyrinogen decarboxylase (E.C. 4.1.1.37, UROD) has been expressed in Escherichia coli and purified to homogeneity. Crystals grew by the hanging-drop vapor-diffusion technique from a starting solution containing 1.5 mg ml−1 protein. The crystals belong to the trigonal space group P3121 or its enantiomer P3221 and diffract to 3 Å resolution. The unit-cell parameters are a = b = 103.4, c = 75.7 Å and γ = 120°. The asymmetric unit contains one molecule. Preliminary structural predictions suggest for the protein a TIM-barrel type tertiary structure.
Crystallization and preliminary X-ray analysis of B-domain fragments of a Staphylococcus aureus collagen-binding protein
Authors: Deivanayagam Champion C. S. , Rich Rebecca L. , Danthuluri Sita , Owens Rick T. , Patti Joseph M. , Höök Magnus , DeLucas Lawrence J. , Narayana Sthanam V. L.
Published: July 2002

Recombinant proteins of monomeric and dimeric B-domain repeats of a Staphylococcus aureus FDA 574 collagen-binding adhesin have been crystallized. The single repeat unit (B1) was crystallized in a body-centered orthorhombic lattice with a = 96.9, b = 101.3, c = 120.8 Å in either the I222 or I212121 space group. These crystals diffracted to 2.5 Å resolution and the calculated Vm
values of 3.2 and 2.2 Å3 Da−1 suggest the possibility of a dimer or a trimer in the asymmetric unit. The two-repeat fragment (B1B2) crystallized in the orthorhombic space group P212121 with cell dimensions a = 42.4, b = 79.4, c = 130.4 Å and diffracted to 2.3 Å resolution. For this species, the calculated Vm
value of 2.2 Å3 Da−1 indicates the presence of a monomer in the asymmetric unit.
Purification and crystallization of a proteolytic fragment of Escherichia coli pyruvate formate-lyase
Authors: Leppänen Veli-Matti , Parast Camran V. , Wong Kenny K. , Kozarich John W. , Goldman Adrian
Published: July 2002

Under anaerobic conditions, the reaction catalysed by pyruvate formate-lyase (PFL) is the first reaction after the production of pyruvate in the glycolytic pathway. Crystallization trials with Escherichia coli PFL were unsuccessful and therefore limited proteolysis was used to produce a stable crystallizable N-terminal protein fragment by trypsin cleavage. The molecular weight of this cleavage product was found to be 69.6 kDa by MALDI MS analysis, and the DNA sequence corresponding to this fragment was cloned. The recombinant protein fragment was crystallized by sitting-drop vapour diffusion using polyethylene glycol 1000 as precipitant. The crystals, which grew to 2 mm in length and 0.2 mm in cross section, belong to the hexagonal space group P61 or P65 with cell dimensions a = b = 140.4, c = 215.3 Å and two molecules per asymmetric unit. X-ray diffraction data were collected from 20 to 3.2 Å resolution from a single frozen crystal on a synchrotron-radiation beamline.
Isomorphous replacement combined with anomalous dispersion in the linear equations: application to a crystal containing four nonapeptide conformers
Authors: Konnert J. , Karle J. , Karle I. L. , Uma K. , Balaram P.
Published: July 2002

The investigation of the structure of the four conformers of the nonapeptide described here has an additional purpose: to illustrate a method for combining isomorphous replacement information with anomalous dispersion information within the linear equations that have found use in the analysis of multiple-wavelength anomalous dispersion data. In the present application, isomorphous replacement data were obtained from the replacement of naturally occurring S atoms in the nonapeptide with Se atoms. Only one wavelength was used for the analysis: Cu Kα radiation. Details of the analysis are presented, as well as the structural results obtained. It was found that the four independent molecules in the structure have similar, but not identical, conformations. The backbones fold into predominantly α-helices with one or two 310-type hydrogen bonds and have extended side chains. Three to four water molecules are associated with each of the four head-to-tail regions between the peptides. Optimal packing between hydrophobic surfaces may account for the existence of four molecules in an asymmetric unit.
Crystallization and preliminary X-ray diffraction studies of blasticidin S deaminase from Aspergillus terreus
Authors: Nakasako Masayoshi , Kimura Makoto , Yamaguchi Isamu
Published: July 2002

Blasticidin S deaminase from Aspergillus terreus was crystallized with polyethylene glycol 8000. Two types of crystals were grown under the same crystallization conditions. One type grew as thin plates, while the other had a rhombic shape. The rhombic shaped crystal was suitable for high-resolution crystal structure analysis. Precession photographs and diffraction data showed that the crystal belonged to orthorhombic space group P212121, with unit-cell dimensions a = 70.33, b = 146.56 and c = 56.48 Å. The calculated Vm
value was acceptable when a tetramer of the enzyme was contained in an asymmetric unit. Preliminary diffraction data were collected to a resolution of 2.0 Å with good statistics.
The structure of plastocyanin from the cyanobacterium Phormidium laminosum
Authors: Bond Charles S. , Bendall Derek S. , Freeman Hans C. , Guss J. Mitchell , Howe Christopher J. , Wagner Michael J. , Wilce Matthew C. J.
Published: July 2002

The crystal structure of the `blue' copper protein plastocyanin from the cyanobacterium Phormidium laminosum has been solved and refined using 2.8 Å X-ray data. P. laminosum plastocyanin crystallizes in space group P43212 with unit-cell dimensions a = 86.57, c = 91.47 Å and with three protein molecules per asymmetric unit. The final residual R is 19.9%. The structure was solved using molecular replacement with a search model based on the crystal structure of a close homologue, Anabaena variabilis plastocyanin (66% sequence identity). The molecule of P. laminosum plastocyanin has 105 amino-acid residues. The single Cu atom is coordinated by the same residues – two histidines, a cysteine and a methionine – as in other plastocyanins. In the crystal structure, the three molecules of the asymmetric unit are related by a non-crystallographic threefold axis. A Zn atom lies between each pair of neighbouring molecules in this ensemble, being coordinated by a surface histidine residue of one molecule and by two aspartates of the other.
Crystallization of hepatitis B virus core protein shells: determination of cryoprotectant conditions and preliminary X-ray characterization
Authors: Wynne S. A. , Leslie A. G. W. , Butler P. J. G. , Crowther R. A.
Published: July 2002

Hepatitis B virus causes liver cirrhosis and hepatocellular cancer and is a major cause of death, particularly in Asia and sub-Saharan Africa. The virus consists of an inner core or nucleocapsid, which encloses the viral nucleic acid, with an outer lipid envelope containing surface-antigen proteins. The core protein, when expressed in E. coli, assembles into spherical shells containing 180 or 240 subunits, arranged with T = 3 or T = 4 icosahedral symmetry. The C-terminal region of the protein is involved in nucleic acid binding, and deletion of this region does not prevent capsid formation. C-terminally deleted hepatitis B core shells containing 240 subunits have been crystallized and data has been collected to 3.6 Å resolution from frozen crystals, using butanediol as a cryoprotectant. The crystals have C2 symmetry, with unit-cell parameters a = 538.0, b = 353.0, c = 369.6 Å, β = 132.3°.
Crystallization and preliminary X-ray analysis of a nitrate reductase from Desulfovibrio desulfuricans ATCC 27774
Authors: Dias João M. , Bursakov Sergey , Carneiro Carla , Moura José J. G. , Moura Isabel , Romão Maria João
Published: July 2002

Periplasmic nitrate reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 contains two molybdopterin guanine dinucleotide cofactors and one [4Fe–4S] cluster as prosthetic groups and catalyzes the conversion of nitrate to nitrite. Crystals of the oxidized form of this enzyme were obtained using PEG as precipitant and belong to space group P3121 or P3221, with unit-cell dimensions a = b = 106.3, c = 135.1 Å. There is one monomer of 80 kDa in the asymmetric unit, which corresponds to a Matthews ratio of 2.75 Å3 Da−1. Using cryo-cooling procedures and X-rays from a rotating-anode generator, diffraction was observed to beyond 3.0 Å resolution.
Crystallization of the oxygen-evolving reaction centre of photosystem II in nine different detergent mixtures
Authors: Adir Noam
Published: July 2002

Oxygen-evolving photosystem II reaction centres (RCII) isolated from both spinach and pea have been crystallized. A single crystal form grew from RCII monomers in the presence of nine different three-component mixtures of non-ionic detergents and heptane-1,2,3-triol. The crystals grew as hexagonal rods with dimensions of up to 1 × 0.3 × 0.3 mm. The crystals diffracted to a maximum resolution of 6.5 Å and belong to a hexagonal space group with unit-cell parameters a = 495, b = 495, c = 115 Å, α = β = 90, γ = 120°. The growth of a single crystal form in the presence of such a large variety of detergents suggests a very limited range of crystal lattice formation sites in the RCII complex.
Crystallization and preliminary X-ray analysis of β-amylase from Bacillus polymyxa
Authors: Yamane Takashi , Tasaki Hiroshi , Matsumoto Fusako , Suzuki Atsuo , Uozumi Nobuyuki , Ashida Tamaichi
Published: July 2002

A truncated β-amylase (E.C. 3.2.1.2) from Bacillus polymyxa has been crystallized using the hanging-drop vapour-diffusion method at 277 K. The crystals belong to the orthorhombic space group P212121 with cell dimensions a = 64.6, b = 141.9, c = 155.1 Å and diffract to 2.5 Å resolution. The asymmetric unit containing three protein molecules was derived from an electron-density map calculated at 4 Å resolution using MIR phases. This gives a Vm
value of 2.36 Å3 Da−1.
N-Acetyl-L-glutamate kinase from Escherichia coli: cloning of the gene, purification and crystallization of the recombinant enzyme and preliminary X-ray analysis of the free and ligand-bound forms
Authors: Gil Fernando , Ramón-Maiques Santiago , Marina Alberto , Fita Ignacio , Rubio Vicente
Published: July 2002

The gene for Escherichia coli
N-acetyl-L-glutamate kinase (NAGK) was cloned in a plasmid and expressed in E. coli, allowing enzyme purification in three steps. NAGK exhibits high specific activity (1.1 µmol s−1 mg−1), lacks Met1 and forms dimers (shown by cross-linking). Crystals of unliganded NAGK diffract to 2 Å and belong to space group P6122 or its enantiomorph P6522 (unit-cell parameters a = b = 78.6, c = 278.0 Å) with two monomers in the asymmetric unit. Crystals of NAGK with acetylglutamate and the ATP analogue AMPPNP diffract to 1.8 Å and belong to space group C2221 (unit-cell parameters a = 60.0, b = 71.9, c = 107.4 Å), with one monomer in the asymmetric unit. NAGK crystallization will allow the determination of proposed structural similarities to carbamate kinase.
Two-wavelength MAD phasing: in search of the optimal choice of wavelengths
Authors: González A. , Pédelacq J.-D. , Solà M. , Gomis-Rüth F. X. , Coll M. , Samama J.-P. , Benini S.
Published: July 2002

The multiwavelength anomalous dispersion (MAD) method is increasingly being used to determine protein crystal structures. In theory, data collection at two wavelengths is sufficient for the determination of MAD phases, but three or even more wavelengths are used most often. In this paper, the results of the phasing procedure using only two wavelengths for proteins containing different types of anomalous scatterers are analyzed. In these cases, it is shown that this approach leads to interpretable maps, similar in quality to those obtained with data collected at three wavelengths, provided that the wavelengths are chosen so as to give a large contrast in the real part of the anomalous scattering factor f. The consequences for a rational MAD data-collection strategy are discussed.
MAD data collection – current trends
Authors: Walsh Martin A. , Evans Gwyndaf , Sanishvili Ruslan , Dementieva Irene , Joachimiak Andrzej
Published: July 2002

The multiwavelength anomalous dispersion (MAD) method of protein structure determination is becoming a routine technique in protein crystallography. The increased number of wavelength-tuneable synchrotron beamlines capable of performing challenging MAD experiments, coupled with the widespread availability of charge-coupled device (CCD) based X-ray detectors with fast read-out times have brought MAD structure determination to a new exciting level. Ultrafast MAD data collection is now possible and, with the widespread use of selenium in the form of selenomethionine for phase determination, the method is growing in popularity. Recent developments in crystallographic software are complementing the above advances, paving the way for rapid protein structure determination. An overview of a typical MAD experiment is described, with emphasis on the rates and quality of data acquisition now achievable at third-generation synchrotron sources.
Expression of a selenomethionyl derivative and preliminary crystallographic studies of human cystatin C
Authors: Kozak Maciej , Jankowska Elzbieta , Janowski Robert , Grzonka Zbigniew , Grubb Anders , Alvarez Fernandez Marcia , Abrahamson Magnus , Jaskolski Mariusz
Published: July 2002

Human cystatin C, a protein with amyloidogenic properties and a potent inhibitor of papain-like mammalian proteases, has been produced in its full-length form by recombinant techniques and crystallized in two polymorphic forms: cubic and tetragonal. A selenomethionyl derivative of the protein, obtained by Escherichia coli expression and with complete Met→Se-Met substitution confirmed by mass spectrometry, amino-acid analysis and X-ray absorption spectra, was crystallized in the cubic form. A truncated variant of the protein, lacking ten N-terminal residues, has also been crystallized. The crystals of this variant are tetragonal and, like the two polymorphs of the full-length protein, contain multiple copies of the molecule in the asymmetric unit, suggesting oligomerization of the protein.
Crystallization and preliminary X-ray diffraction studies on the conserved GTPase domain of the signal recognition particle from Acidianus ambivalens
Authors: Montoya Guillermo , te Kaat Kai , Moll Ralf , Schäfer Günter , Sinning Irmgard
Published: July 2002

The signal recognition particle (SRP) of bacteria consists of only one protein, known as Ffh or the SRP54 homologue, which forms a complex with 4.5S RNA. It also binds to signal peptides and contains a GTPase which displays interesting differences to Ras GTPases. The conserved NG-domain of Ffh from the archaebacterium Acidianus ambivalens was cloned and overexpressed with a C-terminal His tag in Escherichia coli. Crystallization experiments of the native protein as well as of the Thr112Ala mutant, which is deficient in GTP hydrolysis, resulted in crystals suitable for X-ray diffraction. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 64.5, b = 128.3, c = 72.0 Å. At cryogenic temperatures, the crystals diffracted to a resolution limit of 2.8 Å using a rotating-anode generator and contain one molecule per asymmetric unit. A native data set has been collected using synchrotron radiation to around 2.0 Å resolution. Selenomethionine protein was produced; its crystals diffract in-house to about 2.8 Å resolution.
Crystallization and preliminary X-ray diffraction data for a purple acid phosphatase from sweet potato
Authors: Schenk Gerhard , Carrington Lyle E. , Hamilton Susan E. , de Jersey John , Guddat Luke W.
Published: July 2002

Purple acid phosphatase from sweet potato is a homodimer of 110 kDa. Two forms of the enzyme have been characterized. One contains an Fe–Zn centre similar to that previously reported for red kidney bean purple acid phosphatase. Another isoform, the subject of this work, is the first confirmed example of an Fe–Mn-containing enzyme. Crystals of this protein have been grown from PEG 6000. They have unit-cell parameters a = b = 118.4, c = 287.4 Å and have the symmetry of space group P6522, with one dimer per asymmetric unit. Diffraction data collected using a conventional X-ray source from a cryocooled crystal extend to 2.90 Å resolution. The three-dimensional structure of the enzyme will provide insight into the coordination of this novel binuclear metal centre.
Human apolipoprotein A-I: structure determination and analysis of unusual diffraction characteristics
Authors: Borhani David W. , Engler Jeffrey A. , Brouillette Christie G.
Published: July 2002

The crystallization and structure determination of recombinant human apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, is described. The fragment crystallized, residues 44–243 of native apo A-I [apo Δ(1–43)A-I], is very similar to intact native apo A-I in its ability to bind lipid, to be incorporated into high-density lipoproteins and to activate lecithin–cholesterol acyl transferase. Apo Δ(1–43)A-I crystallizes from 1.0–1.4 M sodium citrate pH 6.5–7.5 in space group P212121, with unit-cell parameters a = 97.47, b = 113.87, c = 196.19 Å (crystal form I). The crystals exhibit unusual diffraction intensity spikes and axial extinctions that are discussed in the context of the 4 Å crystal structure. When flash-cooled to 100 K, the crystals diffract synchrotron radiation to 3 Å resolution. Radiation sensitivity and crystal-to-crystal variation have hindered the assembly of a complete 3 Å data set.
Crystallization and preliminary X-ray diffraction studies of cytochrome c
6 from Porphyra yezoensis
Authors: Sasaki Tomokazu , Nakahara Megumi , Matsuda Aya , Yamasaki Takenobu , Katoh Sakae , Ohshima Shigeru , Oonishi Isao , Uchida Akira
Published: July 2002

Cytochrome c
6 from the red alga Porphyra yezoensis has been purified and crystallized by the sitting-drop vapour-diffusion method. Two different crystal forms, tetragonal and orthorhombic, were obtained. The tetragonal crystals belong to space group P41212 or P43212, with unit-cell dimensions a = 49.33 (2), c = 83.70 (10) Å. The orthorhombic crystals belong to space group P212121, with unit-cell dimensions a = 46.74 (2), b = 49.42 (1), c = 37.11 (1) Å. Absorption spectra of the crystals showed that the tetragonal form was oxidized and the orthorhombic form was reduced.
The three-dimensional structure of a Trichoderma reesei β-mannanase from glycoside hydrolase family 5
Authors: Sabini Elisabetta , Schubert Heidi , Murshudov Garib , Wilson Keith S. , Siika-Aho Matti , Penttilä Merja
Published: July 2002

The crystal structure of the catalytic core domain of β-mannanase from the fungus Trichoderma reesei has been determined at a resolution of 1.5 Å. The structure was solved using the anomalous scattering from a single non-isomorphous platinum complex with two heavy-metal sites in space group P21. The map computed with the experimental phases was enhanced by the application of an automated model building and refinement procedure using the amplitudes and experimental phases as observations. This approach is expected to be of more general application. The structure of the native enzyme and complexes with Tris–HCl and mannobiose are also reported: the mannobiose binds in subsites +1 and +2. The structure is briefly compared with that of the homologous β-mannanase from the bacterium Thermomonospora fusca.
Preliminary X-ray crystallographic analysis of a plant defence protein, the polygalacturonase-inhibiting protein from Phaseolus vulgaris
Authors: Leech Andrew , Mattei Benedetta , Federici Luca , De Lorenzo Giuli , Hemmings Andrew M.
Published: July 2002

A leucine-rich repeat plant protein involved in resistance to pathogens, a polygalacturonase-inhibiting protein (PGIP-1) from Phaseolus vulgaris, has been crystallized and preliminary X-ray characterization has been performed. The protein contains ten repeats of a short (24 amino-acid) leucine-rich repeat motif. Single crystals of the protein were grown from vapour-diffusion experiments using PEG 2K monomethylether as precipitant; these crystals diffract to at least 2.3 Å resolution. The space group is P21, with two molecules of PGIP-1 in the asymmetric unit; the crystals contain approximately 38% solvent.
Recent trends of insertion-device technology for X-ray sources
Authors: Kitamura Hideo
Published: July 2002

As a consequence of the developments of in-vacuum undulators, where permanent magnet arrays are located in an ultrahigh vacuum, the in-vacuum mini-gap undulator with very short period has been successful in the X-ray ring of NSLS in collaboration with SPring-8, producing a new concept for synchrotron radiation facilities. The key feature of the concept is the combination of in-vacuum mini-gap undulators and a low-emittance ring with moderate beam energy. In other words there are possibilities for the design of a moderate-cost medium-sized synchrotron radiation facility, the performance of which may be comparable with that of the existing large-scale facilities. Here the performance of in-vacuum undulators is described, particularly of the mini-gap type. Also described is the essence of the new concept for synchrotron radiation facilities, the so-called new third-generation light source.
A study of titanium nitride diffusion barriers between aluminium and silicon by X-ray absorption spectroscopy: the Si, Ti and N results
Authors: Hu Y. F. , Sham T. K. , Zou Z. , Xu G. Q. , Chan L. , Yates B. W. , Bancroft G. M.
Published: July 2002

We report a multi-element, multi-edge and multi-detection mode X-ray photoabsorption study of a series of Al/TiN
x
/Si(100) thin films as a function of the TiNx film thickness (100Å-500Å) and of the annealing temperature (400°C-600°C). The Si K- and L-edge results show that Si does not diffuse to the surface for all the films. The high resolution Ti L-edge and N K-edge spectra show that the TiN
x
layer undergoes a dramatic chemical reaction with the gradual increase in the annealing temperature. This chemical reaction stabilizes at 560°C at which the TiN
x film is known to fail to act as an effective diffusion barrier between Al and Si.
Structural modification on silica glass surface induced by thermal poling for second harmonic generation
Authors: Nazabal V. , Fargin E. , Le Flem G. , Briois V. , Cartier Dit Moulin C. , Buffeteau T. , Desbat B.
Published: July 2002

O-K edge XANES spectroscopy evidences structural modification induced by thermal poling treatment in surfaces of bulk Herasil silica glass presenting second harmonic generation. Considering model silicon dioxide clusters, calculations based on full multiple scattering approach have been performed in order to explain accurately the differences observed on XANES spectra at different stage of the poling treatment. These structural modifications on extreme surface affect both network and defects by breaking Si-O-Si bridging bonds. Despite of the formation of bridging bond occurring during the thermal depoling -which erases the SHG inside the glass-, the initial structure of the unpoled sample is not reproduced.
Speciation of As in the blackfoot disease endemic area
Authors: Wang H.-C. , Wang H. Paul , Peng C.-Y. , Liu S.-H. , Yang Y. W.
Published: July 2002

Speciation of arsenic (As) in well water and contaminated soil in the blackfoot disease endemic area has been studied by extended X-ray absorption fine structural (EXAFS) spectroscopy in the present work. Experimentally, we found that arsenic in the well water possessed an As-O bond distance of 1.72 Å with a coordination number (CN) of 4.3. In the blackfoot disease area, arsenic with a high oxidation state (As(V)) was also observed in the contaminated soil. In the early stage (after 90 minutes) of the electrokinetic remediation (EKR) of the contaminated soil, the in-situ EXAFS data indicated that the CN of As-O (1st shell) decreased slightly, that may be due to the perturbation of the incompact As atoms in the outer shells by EKR.
Anharmonic effective pair potentials of group VIII and Ib fcc metals
Authors: Okube Maki , Yoshiasa Akira
Published: July 2002

The temperature dependence of EXAFS Debye-Waller factors and anharmonic effective pair potentials of group VIII and Ib fcc metals were investigated by a cumulant expansion method. The EXAFS spectra near K- or L3-edges were measured at the temperatures from 30 to 800 K using synchrotron radiation from the Photon Factory, Tsukuba. The effective pair potentials, a˙u2/2! + b˙u3/3! denote that the group Ib has obviously larger anharmonicity than the group VIII metals. The discrepancy between the Morse potential approximation and determined effective pair potential is discussed.
Determination of the iron oxidation state in Earth materials using XANES pre-edge information
Authors: Petit Pierre-Emmanuel , Farges François , Wilke Max , Solé Vincente Armando
Published: July 2002

Fe K-edge XANES spectra have been measured in more than 35 Fe(II) and Fe(III)-bearing minerals. The separation between the average pre-edge centroid positions for Fe(II) and Fe(III) is 1.4 ± 0.1 eV. Examination of calculated pre-edge features of mechanical mixtures of phases containing different proportions of Fe(II) and Fe(III) reveals that different trends of pre-edge position vs. pre-edge intensity can be observed, depending on the coordination environment. Both pre-edge parameters have been used to estimate the ferric/ferrous ratio in 12 natural minerals.
Local structure and oxidation state of Mn and Ni atoms in LaNi1-xMnxO3+δ perovskites
Authors: Sánchez M. C. , Subías G. , Pérez-Cacho J. , García J. , Blasco J.
Published: July 2002

X-ray absorption spectroscopy has been used to study LaNi1-xMnxO3+δ perovskites (x = 0.1, 0.25, 0.5, 0.75, 0.9). We have analysed both, the oxidation state and the local structure around the transition metal atoms. XANES spectra of these samples suggest a mixed valence state for both transition metal atoms. The Mn K-edge is shifted to high energies as the Ni content is increased up to x=0.5. The opposite behavior is found instead, for the Ni K-edge. Samples with x=0.5 and x=0.25 present the Mn K -edge at the same energy but the absorption features are different for both samples. The local structure has also been studied by means of the EXAFS technique. The first coordination shell nicely reflects the structural change observed in this series from rhombohedral perovskites (x>0.5) to orthorhombic perovskites (x<0.5). The changes in the local structure for Ni and Mn atoms agree with the variation of the oxidation state observed in the XANES spectra.
Bond length determination in Cu-Mg-O by EXAFS spectroscopy
Authors: Sidorenko A. F. , Gins K.A. , Babanov Yu.A. , Naumov S.V. , Samokhvalov A.A.
Published: July 2002

Magnetic semiconductors such as Cu
x
Mg1−x
O, which are perspective materials for high-temperature superconductivity have been studied by EXAFS. The new technique of obtaining information from EXAFS-data has been described. It is based on the special iterative algorithm of solving an inverse ill-posed problem on the determination the partial pair correlation functions (pPCFs). Bond lengths of the nearest neighbours have been determined. It was clearly shown that the short range order in compound Cu0.2Mg0.8O differs from a hypothetical alloy with MgO structure and from the copper oxide.
N,N′-Diacetyl-1,13-diaza-24-crown-8
Authors: Bryan Jeffrey C. , Marchand Alan P. , Hazlewood Anna
Published: July 2002

Half of the title compound (N,N′-diacetyl-1,4,7,13,16,19-hexaoxa-10,22-diazacyclotetracosane), C20H38N2O8, makes up the asymmetric unit. The crown ring is relatively flat, and though collapsed in on itself, would require little change to adopt a binding conformation. C—H...O bonding is also observed.
trans-Tetraaquabis(pyridine-3-carboxylate-κN)nickel(II)
Authors: Batten Stuart R. , Harris Alexander R.
Published: July 2002

The title complex, [Ni(C6H4NO2)2(H2O)4], consists of an Ni atom coordinated to twotranspyridinecarboxylate ligands, coordinated through the N atoms, and four water ligands. The Ni atom lies on a site of 2/msymmetry, and the pyridinecarboxylate ligand lies on a mirror plane. Extensive inter-complex hydrogen bonding occurs between the water ligands and the carboxylate groups, resulting in a three-dimensional network.
Redetermination of [bis(2-pyridyl)amine-N,N′]copper(II) diperchlorate
Authors: Du Miao , Bu Xian-He , Weng Lin-Hong , Leng Xue-Bing , Guo Ya-Mei
Published: July 2002

In the crystal structure of the title complex, [Cu(C10H9N3)2](ClO4)2, the CuIIcenter is four-coordinated by the nitrogen donors of the pyridine rings of the ligand, bis(2-pyridyl)amine. The crystal structure reveals that the CuN4coordination sphere has a distorted tetrahedral coordination geometry with a crystallographicC2axis through the CuIIcenter. The perchlorate anions link the complex cations to form a chain structure through C—H...O close contacts and N—H...O hydrogen bonds.
Bis[N-(2-hydroxyethyl)-N-methyldithiocarbamato-S,S′]diphenyltin
Authors: Farina Yang , Baba Ibrahim , Othman A. Hamid , Razak Ibrahim Abdul , Fun Hoong-Kun , Ng Seik Weng
Published: July 2002

The Sn atom in the title compound, [Sn(C6H5)2(C4H8NOS2)2], is six-coordinate in acis–C2SnS4octahedral environment.
The microwave engine
Authors: Kushelev A. , Polyschuk S. , Nedelko E. , Kozhevnikov D. , Pisarzhevsky S.
Published: July 2002

A new type of engine is proposed. The principle of the operation of this engine is as follows. The alternating electric current of high frequency flows from the condenser over the vertical conductor of the cross and branches at its centre in three directions. The vertical current generates a magnetic field. The horizontal currents flow in counter‐directions; therefore their magnetic fields are mutually cancelled, but the side branches of the cross are subjected to the operation of the Ampere force (F) from the magnetic field of the vertical conductor. This force moves the engine forward.