bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical prediction of bond-valence networks. II. Comparison of the graph-matrix and resonance-bond approaches. Erratum
Authors: Rutherford John S.
Published: July 2002

The correct version of Fig. 2 in the paper by Rutherford [Acta Cryst. (1998), B54, 204–210] is given. It shows that, assuming graph-equivalent bonds are equal, there are 57 possible bond-length sequences for β-Ga2O3 within the constraints of the Valence-Sum Rule.
Metastructures: homeomorphisms between complex inorganic structures and three-dimensional nets
Authors: Schindler M. , Hawthorne F. C. , Baur W. H.
Published: July 2002

We propose a general approach to nets and structures in which vertices represent stereochemically significant groups or clusters of atoms, and edges represent the linkage between these groups. Vertices may be single atoms, dimers, coordination polyhedra, clusters of atoms or clusters of coordination polyhedra; edges may be single chemical bonds or sets of several chemical bonds. Thus, a single net may be the basis for a family of structures that are homeomorphic to that net. The coordination of polyhedra or units around a vertex is visualized by connecting the centres of the atoms or groups at the vertices connected with the central vertex. Thus, the concept of coordination number is extended to include coordinating groups. We name a net after a homeomorphic simple structure-type for which there is a one-to-one correspondence between the vertices of the net and specific atoms of the structure, and between the edges of the net and the chemical bonds. We term the resulting more complex structures metastructures in order to distinguish them from their corresponding simple structure-types. Individual metastructures are referred to as alpha structures similar to a particular simple type. Thus, the open complex framework of [V5O9(PO4)2] composition in microporous Na
v
[((V^{4+}_{4-w}V^{5+}_{1+w})O9)(PO4)2]·(PO4)
x
·(OH)
y
·zH2O is an α-NbO structure based on the simple net that is homeomorphic to NbO. This approach is effective in hierarchically classifying both simple close-packed structures and very complicated microporous structures.
Packing effects on the geometry of neutral platinum(II) complexes due to solvate molecules: the structure of trans-dichlorobis(triphenylarsine)platinum(II)
Authors: Johansson Maria H. , Otto Stefanus , Roodt Andreas , Oskarsson Åke
Published: July 2002

A series of structures of trans-dichlorobis(triphenylarsine)platinum(II), recrystallized from four different solvents, have been characterized by X-ray crystallography and were shown to crystallize as different solvates (same metal complex, different crystallization solvents). Their geometric differences induced by packing and solvent molecules were analysed with half-normal probability plots and root-mean-square deviations. The recrystallization solvents used in the investigation were 1,1,1-trichloroethane, dichloromethane, 1,2-dichloroethane and benzene, and the following crystallization modes were obtained. From 1,1,1-trichloroethane the metal complex crystallizes without solvent as trans-[PtCl2(AsPh3)2] in P21/n with Z = 2, a = 9.271 (2), b = 19.726 (4), c = 9.830 (2) Å, β = 111.83 (3)°, V = 1668.8 (6) Å3, R = 0.0262, and from dichloromethane with two solvent molecules as trans-[PtCl2(AsPh3)2]·2CH2Cl2 in Pbca with Z = 4, a = 20.582 (4), b = 8.146 (2), c = 23.491 (5) Å, V = 3938.5 (14) Å3 and R = 0.0316. From dichloroethane it crystallizes with one solvent molecule as trans-[PtCl2(AsPh3)2]·C2H4Cl2 in P\overline 1 with Z = 1, a = 9.390 (2), b = 9.548 (2), c = 11.931 (2) Å, α = 109.70 (3), β = 108.26 (3), γ = 98.77 (3)°, V = 915.6 (3) Å3, R = 0.0390, and from benzene with half a solvent molecule as trans-[PtCl2(AsPh3)2]·0.5C6H6 in P21/n with Z = 4, a = 11.778 (2), b = 18.712 (4), c = 16.647 (3) Å, β = 104.78 (3)°, V = 3547.3 (12) Å3 and R = 0.0303. In all four compounds platinum(II) coordinates to triphenylarsine and chloride in a pseudo-square-planar trans configuration. The Pt—As distances are in the range 2.4104 (4)–2.3923 (4) Å and the Pt—Cl distances are in the range 2.309 (2)–2.2839 (9) Å. The solvents have a large influence on the packing, resulting in different space groups or different occupancies in the same space group. Half-normal probability plots show that the largest geometric differences, within the metal complex, are in the bond and torsion angles around the As—C bonds. Very similar torsion angles were observed around the Pt—As bond for all the structures, except for one AsPh3 ligand in the benzene solvate, which differs by about 10° from the others. The metal–donor bond distance varies by as much as 0.019 and 0.025 Å (95% confidence interval) for Pt—As and Pt—Cl, respectively. The variations are essentially caused by intermolecular interactions. Packing efficiency is expressed as the volume filled by each metal complex in the unit cell and is calculated by subtracting the sum of the solvent molecule volumes from the total volume of the unit cell and then dividing by Z. The efficiency is largest in the dichloroethane solvate and smallest in the non-solvated compound, with a difference of approximately 22 Å3 per metal complex.
High-pressure transformations of NbO2F
Authors: Carlson Stefan , Larsson Ann-Kristin , Rohrer Franziska E.
Published: July 2002

The ReO3-type structure NbO2F, niobium dioxyfluoride, has been studied at high pressures using diamond anvil cells and synchrotron X-ray radiation. High-pressure powder diffraction measurements have been performed up to 40.1 GPa. A phase transition from the cubic (Pm3¯m) ambient pressure structure to a rhombohedral (R3¯c) structure at 0.47 GPa has been observed. Rietveld refinements at 1.38, 1.96, 3.20, 6.23, 9.00 and 10.5 GPa showed that the transition involves an a
−
a
−
a
− tilting of the cation–anion coordination octahedra and a change of the anion–anion arrangement to approach hexagonal close packing. Compression and distortion of the Nb(O/F)6 octahedra is also revealed by the Rietveld refinements. At 17–18 GPa, the diffraction pattern disappears and the structure becomes X-ray amorphous.
Symmetry and twins in the monophosphate tungsten bronze series (PO2)4(WO3)2m
(2 ≤ m ≤ 14)
Authors: Roussel Pascal , Labbé Philippe , Groult Daniel
Published: July 2002

Monophosphate tungsten bronze with pentagonal tunnels (PO2)4(WO3)2

m
are low-dimensional materials with charge density wave (CDW)-type electron instabilities. Two forms of the structure can thus be expected for all the members of the series: a low-temperature form (LT) corresponding to the CDW state and a high-temperature form (HT) corresponding to a normal metallic state. The HT form is described here for m = 9 and compared with that of the m = 5 and m = 7 counterparts. It is shown that a systematic twin phenomenon must be taken into account for HT members because of two possible configurations of the tilting mode of WO6 octahedra. The structure is also compared with that of m = 10, which exhibits the modulated CDW–LT form at room temperature. Owing to two possible polarization directions of the segments built of m WO6 octahedra, a twin phenomenon is also encountered in the LT forms. A review of all the structures known at present (m = 2, 4, 5, 6, 7, 8, 9, 10, 12) leads us to propose a structural law based on the building mode of WO6 octahedra in WO3-type slabs to explain the symmetry changes observed between even and odd members of the series.
Classes d'éléments conjugués des groupes cristallographiques
Authors: Sivardière J.
Published: July 2002

Let G be a finite group, H an invariant subgroup and F the corresponding factor group. The classes of conjugated elements of G are derived from the classes of H and F. We consider simple point groups and symmorphic space groups, which are semi-direct products H^F, then double point groups and non- symmorphic space groups, which are extensions of F by H.
An alternative to Hamilton's R-factor ratio test with special application to atom-assignment problems in crystallography
Authors: Rothstein S. M. , Richardson M. F. , Bell W. D.
Published: July 2002

A procedure is given for estimating the variance ratio σ
2
1/σ
2
11, of two models of a crystal structure where σ
2
1 and σ
2
11 are the variances of the weighted (|Fo
| - |Fc
|) distributions for models I and II, respectively, and |Fo
| and |Fc
| are the observed and calculated structure factors. The procedure provides a statistical test of the hypothesis that the above ratio is unity for a given pair of models and, thus, whether one of the models offers a significantly better description of the crystal structure. The method is applicable to crystallographic problems in which each of two or more structural models is expressed in terms of the same set of parameters. It has been applied to a number of atom-assignment problems, and the results are compared with those from Hamilton's R-factor ratio test.
Crystal powder statistics. II. Line profiles in diffraction spectra of identical crystals and of Gaussian samples. Crystal size distributions
Authors: Allegra G. , Ronca G.
Published: July 2002

The average interference function ({\cal J}
hkl
(ΔS)) of a powder sample containing perfect crystals at a reciprocal distance ΔS from the peak is evaluated both for the case of identical parallelepiped crystals and for a Gaussian sample [probability of thickness d along a given crystal direction = C1 exp (-C
2
d
2)]. In the latter case ({\cal J}
hkl
(ΔS)) decreases as 1/ΔS
2 for large ΔS, by analogy with the Bernoullian model [Ailegra, Bassi & Meille (1978). Acta Cryst. A34, 652-655] although with a smaller amplitude, for a fixed integrated intensity and half-peak width. It is shown that the Gaussian interference function, or line profile, cannot be given by any real sample, at least if its crystals neither contain holes nor have concave surfaces. Number and weight probability distributions are calculated both for the Bernoullian and for the Gaussian crystal-size statistics. As expected from the calculated line profiles, the Bernoullian statistics correspond to a larger weight percentage of crystals smaller than the average.
On `non-stoichiometric phases' in thin films of rare-earth oxides
Authors: Gasgnier M. , Caro P.
Published: July 2002

Kaul & Saxena [Acta Cryst. (1977), A33, 992-996] have reported the existence of long-range and short-range order in a non-stoichiometric phase 'LnO
x
' (Ln = rare earth). It is shown that the experiments they are describing are indeed the oxidation of the rare-earth hydride LnH2 into the rare-earth cubic C-type sesquioxide. The interpretation they give of their experiments is to be discarded entirely.
Modelling prior distributions of atoms for macromolecular refinement and completion
Authors: Roversi Pietro , Blanc Eric , Vonrhein Clemens , Evans Gwyndaf , Bricogne Gérard
Published: July 2002

Until modelling is complete, macromolecular structures are refined in the absence of a model for some of the atoms in the crystal. Techniques for defining positional probability distributions of atoms, and using them to model the missing part of a macromolecular crystal structure and the bulk solvent, are described. The starting information may consist of either a tentative structural model for the missing atoms or an electron-density map. During structure completion and refinement, the use of probability distributions enables the retention of low-resolution phase information while avoiding premature commitment to uncertain higher resolution features. Homographic exponential modelling is proposed as a flexible, compact and robust parametrization that proves to be superior to a traditional Fourier expansion in approximating a model protein envelope. The homographic exponential model also has potential applications to ab initio phasing of Fourier amplitudes associated with macromolecular envelopes.
Density constraints and low-resolution phasing
Authors: Urzhumtsev Alexandre G. , Lunina Natalia L. , Skovoroda Tatiana P. , Podjarny Alberto D. , Lunin Vladimir Y.
Published: July 2002

Direct phasing needs additional information of a non-specific kind in order to select the correct phase set from all possible ones. This paper analyses the use of constraints which can be formulated in terms of electron-density values. One- and multi-dimensional histograms and connectivity properties are implemented as such constraints in density-modification procedures. These approaches usually cannot unambiguously select the best solution from a set of alternative phase variants. Nevertheless, they do allow the rejection of wrong solutions and the use of cluster analysis and averaging on the remaining variants provide a good starting point for further phase-refinement procedures.
Rotations and rotation matrices
Authors: Evans Philip R.
Published: July 2002

In molecular replacement, a model, described as a list of orthogonal coordinates, is to be moved into a new position and orientation. The orthogonal coordinate system also has to be related to the crystallographic system, which may not be orthogonal, and crystallographic symmetry must be considered, which applies to coordinates expressed as fractions of the unit cell. Elementary properties of rotation matrices and their representation as polar or Eulerian angles are discussed.
NMR trial models: experiences with the colicin immunity protein Im7 and the p85α C-terminal SH2–peptide complex
Authors: Pauptit Richard A. , Dennis Caitríona A. , Derbyshire Dean J. , Breeze Alexander L. , Weston Simon A. , Rowsell Siân , Murshudov Garib N.
Published: July 2002

Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85α subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excized. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.
Creating structure features by data mining the PDB to use as molecular-replacement models
Authors: Oldfield T. J.
Published: July 2002

Mathematical data-mining techniques to generate a representative set of protein fragments are described. Protein fragments are used as search models within the macromolecular phasing method of molecular replacement to attempt to phase protein data without a homologous model correctly. Preliminary investigations using these fragments indicate that molecular replacement with AMoRe is not sensitive enough to phase myoglobin or insulin data sufficiently for successful refinement. The results suggest that more advanced molecular replacement techniques may be successful, though at present these are not computationally practical.
Crystallization and preliminary crystallographic investigation of porcine quinolinate phosphoribosyltransferase
Authors: Moore Dwight , Bice Todd , Jin Le , Grandhi Asha , DeLucas Lawrence J. , Narayana Sthanam V. L.
Published: July 2002

Quinolinate phosphoribosyltransferase (QPRT), purified from hog liver, has been crystallized using PEG 8000 as the precipitant. The crystals form long hexagonal rods in the space group P6322 with cell dimensions a = b = 121.7, c = 94.5 Å. Based on the unit-cell dimensions and the calculated molecular mass of 33 500 Da, the Matthews coefficient suggests one molecule per asymmetric unit (Vm
= 3.45 Å3 Da−1; 64% solvent). Three native data sets were collected to a resolution of 2.5 Å and merged to provide a set that is 94.7% complete, with an R
sym value of 9.6%.
Structure Determination of Echovirus 1
Authors: Filman D. J. , Wien M. W. , Cunningham J. A. , Bergelson J. M. , Hogle J. M.
Published: July 2002

The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 Å resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 Å. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 Å resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.
Structure of the Mutant E92K of [2Fe–2S] Ferredoxin I from Spinacia oleracea at 1.7 Å Resolution
Authors: Binda Claudia , Coda Alessandro , Aliverti Alessandro , Zanetti Giuliana , Mattevi Andrea
Published: July 2002

Ferredoxin I (Fd I) from Spinacia oleracea is composed of 97 amino-acid residues and a [2Fe–2S] cluster. The crystal structure of the E92K mutant of Fd I was solved by molecular replacement and refined to an R factor of 19.6% for 11755 reflections at 1.7 Å resolution. The overall structure and the active centre of spinach Fd is highly conserved with respect to ferredoxins of known structure. The E92K mutation appears to disturb a hydrogen-bond network which stabilizes the loop bearing the [2Fe–2S] cluster. This observation provides a rationale for the reduced electron-transfer efficiency displayed by the E92K mutant. Inspection of the crystal packing reveals that the side chain of Lys92 is engaged in an intermolecular interaction with Asp26 of a symmetry-related molecule. This feature may explain why only the mutant E92K and not wild-type Fd I could be successfully crystallized.
Crystallization and preliminary X-ray diffraction studies of α-toxin from two different strains (NCTC8237 and CER89L43) of Clostridium perfringens
Authors: Basak A. K. , Howells A. , Eaton J. T. , Moss D. S. , Naylor C. E. , Miller J. , Titball R. W.
Published: July 2002

The α-toxin of Clostridium perfringens is the major virulence determinant for gas gangrene in man. The gene encoding the α-toxin has been cloned into E. coli from two strains of the bacterium (NCTC8237 and CER89L43) and subsequently purified to homogeneity. The two strains of α-toxin differ by five amino acids, resulting in the toxin from NCTC8237 being sensitive to chymotrypsin digestion while that from CER89L43 is resistant. The α-toxin from each of these strains has been crystallized in two different forms by the hanging-drop vapour-diffusion method at 293 K. CER89L43 form I crystals belong to space group R32 and have two molecules in the crystallographic asymmetric unit and a unit cell with a = b = 151.4, c = 195.5 Å, α = β = 90, γ = 120°. The crystals diffracted to d
min = 1.90 Å. The characteristics of the NCTC8237 form I crystals have already been reported. The form II crystals from both strains belong to space group C2221 with one molecule in the crystallographic asymmetric unit and, for strain CER89L43, have cell dimensions a = 61.05, b = 177.50, c = 79.05 Å, α = β = γ = 90°, while for strain NCTC8237 the cell dimensions are a = 60.50, b = 175.70, c = 80.20 Å, α = β = γ = 90°. The crystals diffracted to maximum resolutions of 1.85 and 2.1 Å for the CER89L43 and the NCTC8237 strains, respectively.
Solution of the structure of the cofactor-binding fragment of CysB: a struggle against non-isomorphism
Authors: Verschueren Koen H. G. , Tyrrell Richard , Murshudov Garib N. , Dodson Eleanor J. , Wilkinson Anthony J.
Published: July 2002

The elucidation of the structure of CysB(88–324) by multiple isomorphous replacement (MIR) techniques was seriously delayed by problems encountered at every stage of the analysis. There was extensive non-isomorphism both between different native crystals and between native and heavy-atom-soaked crystals. The heavy-atom substitution was invariably weak and different soaking experiments frequently led to substitution at common sites. These correlated heavy-atom binding sites resulted in an overestimation of the phase information. Missing low-resolution reflections in the native data set, constituting only 2% of the total observations, reduced the power of density modification and phase refinement. Finally, the extensive dimer interface made it difficult to isolate a single molecule in the course of model building into the MIR maps. The power of maximum-likelihood refinement (REFMAC) was exploited in solving the structure by means of iterative cycles of refinement of a partial model, initially comprising only 30% of the protein atoms in the final coordinate set. This technique, which uses experimental phases, can automatically discriminate the correct and incorrect parts of electron-density maps and give properly weighted combined phases which are better than the experimental or calculated ones. This allowed the model to be gradually extended by manual building into improved electron-density maps. A model generated in this way, containing just 50% of the protein atoms, proved good enough to find the transformations needed for multi-crystal averaging between different crystal forms. The averaging regime improved the phasing dramatically such that the complete model could be built. The problems, final solutions and some possible causes for the observed lack of isomorphism are discussed.
Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms
Authors: Misaki Shintaro , Morimoto Yukio , Ogata Mari , Yagi Tatsuhiko , Higuchi Yoshiki , Yasuoka Noritake
Published: July 2002

The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 Å; form II, P21, a = 27.3, b = 44.9, c = 51.2 Å and β = 90.6°) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 Å to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 Å resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 32 symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 32 axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.
Plasminogen activator inhibitor 1 (PAI-1) in its active conformation: crystallization and preliminary X-ray diffraction data
Authors: Willems Pieter K. A. , Rabijns Anja , Aertgeerts Kathleen , Vleugels Nele , Knockaert Isabelle , De Bondt Hendrik L. , De Ranter Camiel J. , Declerck Paul J.
Published: July 2002

Because of its intrinsic lability, wild-type plasminogen activator inhibitor 1 (PAI-1) cannot be crystallized in its active conformation. Therefore, a stable variant of PAI-1 was used to retain the active conformation during crystallization. Four different crystallization conditions were evaluated in detail and two major types of crystals were detected. Whereas solutions consisting of either (i) cacodylate and sodium acetate, (ii) lithium sulfate and polyethylene glycol 4K, or (iii) imidazole, sodium chloride and sodium potassium phosphate buffer revealed thin platelet crystals, a solution (iv) containing ammonium acetate, citrate and polyethylene glycol 4K appeared to enhance the formation of clustered brush-like crystals. Crystals grown under condition (iii) were found to be suitable for X-ray data collection and consequent structural investigation. Data collection was 79.8% complete with a maximum resolution of 2.92 Å. Importantly, PAI-1 retained its functional properties under all conditions.
Preliminary crystallographic studies on glutamine synthetase from Mycobacterium tuberculosis
Authors: Gill Harindarpal S. , Pfluegl Gaston M.U. , Eisenberg David
Published: July 2002

The etiologic agent of tuberculosis, Mycobacterium tuberculosis, has been shown to secrete the enzyme glutamine synthetase (TB-GS) which is apparently essential for infection. Four crystal forms of a recombinant TB-GS were grown. The one chosen for synchrotron X-ray data collection belongs to space group P212121 with unit-cell dimensions 208 × 258 × 274 Å, yielding 2.4 Å resolution data. A Matthews number of 2.89 Å3 Da−1 is found, corresponding to 24 subunits of molecular mass 1300 kDa in the asymmetric unit. From earlier work, the structure of Salmonella typhimurium GS, which is 51% identical in sequence to TB-GS, is known to be dodecameric with 622 symmetry. Self-rotation calculations on the TB-GS X-ray data reveal only one set of sixfold and twofold axes of symmetry. A Patterson map calculated from the native X-ray data confirms that there are two dodecamers in the asymmetric unit, having both their sixfold and twofold axes parallel to one another.
A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences
Authors: Christlet T. Hema Thanka , Biswas M. , Veluraja K.
Published: July 2002

An analysis of the frequency of occurrence of various residues at position X was carried out on the consensus glycosylating sequence Asn-X-Ser/Thr using the PDB three-dimensional database. 488 non-homologous proteins bearing 696 Asn-X-Ser/Thr (X ≠ Pro) sequences were analysed. More than 65% of Asn residues, when they occur as part of the consensus sequence, lie on the surface of the protein, implying a potentiality for glycosylation. A deviation parameter (DP) was calculated as a measure of preferential (positive) or non-preferential (negative) selection. At the X position in the consensus-sequence segment, the amino acids Gly, Asn and Phe have statistically significant positive DP values. The high value of DP for Asn is a consequence of the preferential occurrence of homodoublets, while for Phe it may be a consequence of the stacking interaction of the aromatic ring with the glycan. Gly at the X position in the consensus glycosylating sequence may be functionally significant owing to its preference and its high percentage of occurrence in proteins. The Ramachandran (Φ,Ψ) angles around Gly in the consensus sequence show clustering in the region which is disallowed for non-glycyl residues. In this region, a hydrogen bond between the side chain of Asn and the peptide backbone/side chain of Ser/Thr is possible, reflecting a positional as well as a conformational role in the consensus glycosylating sequence. For the 44 confirmed N-glycosylating sequences, an in-depth analysis of the (Ψ
N
, Φ
X
, Ψ
X
, Φ
S/T
) dihedral angles, which position the side chains of Asn and Ser/Thr, shows that these can be grouped into nine conformational states. In most cases, a direct or water-mediated hydrogen bond between OD1 of Asn and OG of Ser/Thr is possible, reflecting the possible importance of this hydrogen bonding in the glycosylation process.
Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 Å structure solution
Authors: Yu-dong Liu , Harvey I. , Yuan-xin Gu , Chao-de Zheng , Yi-zong He , Hai-fu Fan , Hasnain S. S. , Hao Q.
Published: July 2002

The structure of rusticyanin is the largest unknown structure (Mr
= 16.8 kDa) which has been recently solved by the direct-methods approach using only single-wavelength anomalous scattering (SAS) data from the native protein [Harvey et al. (1998). Acta Cryst. D54, 629–635]. Here, the results of the Sim distribution approach [Hendrickson & Teeter (1981). Nature (London), 290, 107–113] and of the CCP4 procedure MLPHARE [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763] are compared with those from direct methods. Analysis against the final refined model shows that direct methods produced significantly better phases (average phase error 56°) and therefore significantly better electron-density maps than the Sim distribution and MLPHARE approaches (average phase error was around 63° in both cases).
Crystal engineering: deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus
Authors: Dale Glenn E. , Kostrewa Dirk , Gsell Bernard , Stieger Martin , D'Arcy Allan
Published: July 2002

The 24 kDa fragment of DNA gyrase B from Staphylococcus aureus was expressed in Escherichia coli and purified for crystallization. Crystals of the wild-type protein grew in the presence of cyclothialidine but proved difficult to reproduce. In order to improve the crystallization, the flexible regions of the protein were deleted by mutagenesis. The mutant proteins were analyzed by differential scanning calorimetry and the most stable mutants produced crystals. It was possible to reproducibly grow in the microbatch system single well defined crystals which belonged to the space group C2 and diffracted isotropically to approximately 2 Å resolution.
Matching X-ray source, optics and detectors to protein crystallography requirements
Authors: Nave Colin
Published: July 2002

A review of the requirements for collecting X-ray diffraction data from protein crystals is given, with an emphasis on the properties of the crystal and its diffraction pattern. The size, unit-cell dimensions and perfection of the crystals can all be related to the required size and divergence of the incident X-ray beam, together with the size and spatial resolution of the detector. The X-ray beam causes primary radiation damage, even in frozen crystals. If the incident beam is very intense, temperature rises and gradients could occur in the crystal. The extent to which these problems can be overcome is also discussed.
Refined structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli at 1.57 Å resolution
Authors: Kato Masato , Mizuno Takeshi , Shimizu Toshiyuki , Hakoshima Toshio
Published: July 2002

The crystal structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli has been refined to 1.57 Å resolution, using the coordinates of the earlier 2.06 Å structure as a starting model. The final model contained 956 protein atoms, one zinc ion and 156 water molecules, with an R factor of 19.0%. The high-resolution electron-density maps clearly revealed additional solvent molecules and seven discrete rotamers in the protein side chains. One residue, Met755, was fully buried but was able to occupy the space in the hydrophobic core by means of the two-state conformation of its side chain. One water molecule was buried in the protein core and contributed to the rigidity of the HPt domain, cooperating in the coordination of the zinc ion.
Crystallization and preliminary X-ray analysis of a bacteriophage T4 primase fragment
Authors: Korndörfer Ingo P. , Salerno Jeffrey , Jing Debra , Matthews Brian W.
Published: July 2002

The primase from bacteriophage T4 is a single-stranded DNA-dependent RNA polymerase that is one of the seven proteins that constitute the DNA-replication machinery of bacteriophage T4. In an attempt to crystallize the protein, a number of variants were generated. One such construct, which includes the C-terminal region (residues 196–340), gave four different crystal forms which diffract in the 3.5–6.0 Å resolution range.
A new model for statistical error analysis in XAS: about the distribution function of the absorption coefficient
Authors: Curis Emmanuel , Bénazeth Simone
Published: July 2002

Under some general hypothesis, this paper proposes a theoretical model, showing that a gaussian distribution is generally a good approximation of the experimental distribution of the absorption coefficient. This result is confirmed experimentally by usage of appropriate statistical tests.
EXAFS analysis using FEFF and FEFFIT
Authors: Newville Matthew
Published: July 2002

Some of the advanced EXAFS analysis features of FEFF and FEFFIT are described. The scattering path formalism from FEFF and cumulant expansion are used as the basic building blocks of EXAFS analysis, giving a flexible and robust parameterization of most EXAFS problems. The ability to model EXAFS data in terms of generalized physical variables is shown, including the simultaneous refinement of two different polarizations for Co K EXAFS data of \rm CoPt_{3}.
Soft X-ray spectromicroscopy of polymers and biopolymer interfaces
Authors: Hitchcock Adam P.
Published: July 2002

The status of soft X-ray spectromicroscopy (near edge X-ray absorption, or NEXAFS, microscopy) is summarized, with particular emphasis on recent collaborative studies carried out by the author's group at the scanning transmission X-ray microscopy (STXM) and the photoelectron emission microscopy (PEEM) instruments at the Advanced Light Source. Results described include: characterization of phase segregation and filler particles in polyurethanes; effects of confinement on polymer self-organization; characterization of chemically structured polyurea capsule walls; and preferential interactions of proteins with chemically heterogeneous polymer surfaces. The latter is part of a systematic study of the biocompatibility of polymers used in blood contact applications.
EXAFS study of NiAl in thin films
Authors: Arčon Iztok , Mozetič Miran , Kodre Alojz , Jagielski Jacek , Traverse Agnes
Published: July 2002

Technologically important coatings of transition-metal aluminides can be produced by thermal or ion beam mixing of multilayer structures sputter deposited on substrates. The quantitative detection of constituents by depth profiling is sufficient to establish the efficiency of mixing methods. However, to decide whether a mixture of nanoparticles or a stoichiometric alloy is formed, EXAFS analysis of the local atomic neighborhood in the film is required. Ni K edge EXAFS spectra are measured on a series of samples of Ni/Al multilayer on Si(111) surface, after ion mixing at different substrate temperatures. The spectra show that with increasing temperature the nickel aluminide phase gradually substitutes the Ni fcc metal phase.
XAS investigation of Al2O3-coated nano-composite ZrO2
Authors: Hagelstein Michael , Moser Herbert O. , Vollath Dieter , Ferrero Claudio , Borowski Michael
Published: July 2002

In order to complement the structural characterisation by high resolution electron microscopy and perturbed angular correlation spectroscopy (PAC) of Al2O3 coated nano-composite ZrO2, XAFS spectra have been acquired and analysed. The electron micrographs showed fringes of a well ordered lattice and well defined crystal faces of the as-produced powder whereas the PAC spectra indicated a strongly distorted short range order. On the basis of the XAFS data, a structural model for the ZrO2 core of the nano-composite ZrO2/Al2O3 with a well ordered Zr lattice and a sevenfold, strongly distorted nearest neighbour oxygen shell is proposed. A smooth temperature dependence without an indication for a phase transformation up to a temperature of 700K has been revealed.
Structural analysis of La/Al2O3 catalysts by La K-edge XAFS
Authors: Yamamoto Takashi , Tanaka Tsunehiro , Matsuyama Takahiro , Funabiki Takuzo , Yoshida Satohiro
Published: July 2002

Structural analysis of La/Al2O3 catalyst materials was carried out by means of XRD and La K-edge XAFS. Influences of loading amounts and treatment temperature on the local structure around La were investigated. La atoms are supported on γ-Al2O3 in a highly dispersed form when a loading amount is less than 0.2 mmol g(Al2O3)-1, and structural transformation of the La species does not take place in the temperature ranges of 873-1273 K. La species of highly loaded catalysts start to change their structure from oxide-like form to the aluminate at 1073 K. Formation of LaAlO3 perovskite on the catalyst surface requires a concentration of La atoms above 0.5 mmol g(Al2O3)−1 (7.5 wt% as La2O3).
XAFS study on metal endohedral fullerenes
Authors: Kubozono Yoshihiro , Inoue Takashi , Takabayashi Yasuhiro , Fujiki Satoshi , Kashino Setsuo , Akasaka Takeshi , Wakahara Takatsugu , Inakuma Masayasu , Kato Haruhiko , Sugai Toshiki , Shinohara Hisanori , Emura Shuichi
Published: July 2002

Structure of metal endohedral fullerenes is studied by XAFS and XANES. The Sc-Sc distance of 2.23(1) Å determined from Sc K-edge XAFS supports the formation of a triangular Sc3 cluster in Sc3@C82 as is found by MEM analysis for the X-ray diffraction. Gd LIII-edge XAFS of Gd@C82 shows that the first and the second neigboring Gd-C distances are 2.51(2) and 2.85(4) Å, respectively. The La-La distance of La2@C80 has been determined to be 3.90(1) Å at 40 K. This value does not change when increasing temperature [3.90(2) Å at 240 K]. The position and the valenece of the Eu atom in Eu@C60 are also discussed based on Eu LIII-edge XAFS and XANES.
XAS applied to pharmaceuticals: drug administration and bioavailability
Authors: Nicolis Ioannis , Deschamps Patrick , Curis Emmanuel , Corriol Odile , Acar Valérie , Zerrouk Naïma , Chaumeil Jean-Claude , Guyone François , Bénazeth Simone
Published: July 2002

We present selected XAS applications, focused towards practical hospital questions of drug administration and bioavailability, where the technique is driven up to its limits of sensitivity. i) XAS was used to study the interactions between the components of parenteral nutrition solutions, in particular zinc and aminoacids, possibly modifying their bioavailability. ii) We studied by EXAFS a series of binary and ternary copper-aminoacid complexes, in view of the development of an efficient oral drug against copper deficiencies in Menkes disease. iii) EXAFS and XANES analysis allowed us to characterise the solution form of a new arsenic containing drug against leukaemia. In parallel to the XAS measurements, we analysed trace elements levels along patients' hairs, using X-ray fluorescence excited by synchrotron radiation. The measurements along the hair allow for a monitoring of essential trace elements during therapy.
Li K-edge spectra of lithium halides
Authors: Tsuji J. , Kojima K. , Ikeda S. , Nakamatsu H. , Mukoyama T. , Taniguchi K.
Published: July 2002

We measured the Li K-edge spectra of lithium halides by means of total electron yield method (TEY), using the soft x-ray Beam Line 2 (BL2) of the compact synchrotron radiation facility at Ritsmeikan University in Japan. In lithium halides, the spectra have a sharp peak at about 60eV and a broad peak at the higher energy side. Various peak structures that appear in the absorption spectra are assigned to the corresponding Li-1s to valence band free orbitals transitions, which have been calculated by the Discrete Variational (DV)-Xα molecular orbital calculation method.
In situ and ex situ XANES study of nanodispersed Mo species in zeolites used in fine chemistry catalysis
Authors: Rentería Mario , Traverse Agnès , Anunziata Oscar A. , Lede Eduardo J. , Pierella Liliana , Requejo Félix G.
Published: July 2002

Mo K-edge XANES experiments on Mo-containing zeolites at low Mo loading (1 and 2 wt% of Mo on H-ZSM-11, H-BETA and H-ZSM-5 catalysts), active in fine chemistry reactions, were performed ex situ as function of sample calcination temperature in air (in the range 773-973 K) or in situ at 873 and 973K under N2 flow. The results showed a 4-fold oxygen coordination for the incorporated Mo species in the activated (dehydrated) state. Combining these results with additional data evidences an almost total Mo exchange inside the zeolite channels.
A quasi-solid state electrochemical cell for in situ EXAFS measurements on biological samples
Authors: Cognigni Andrea , Ascone Isabella , Zamponi Silvia , Marassi Roberto
Published: July 2002

A new `quasi-solid state' spectroelectrochemical cell for in situ XAS measurements is described and tested using microperoxidase as reference material. The cell substantially improves conventional thin layer cells used for solution XAS spectroelectrochemistry in terms of assembling time and, more important, equilibration of the redox system under study with the applied potential. Spectra can be, in fact, recorded simultaneously during a slow scan rate cyclic voltammetric scan thus permitting correlation of the spectra and the electrochemical curve. Other advantages are the possibility to use very small quantities of material also with second-generation rings. With high intensity sources having focussed beams a further decrease of the specimen weight can be easily obtained and the acquisition time of spectra further reduced.
Electronic structure investigation of Mg1-x
Fe
x
S solid solution: X-ray absorption study
Authors: Stekhin I. E. , Soldatov A. V. , Farrell S. P. , Fleet M. E.
Published: July 2002

X-ray absorption fine structure at the sulfur K edge in Mg1-x
Fe
x
S solid solution (0 ≤ x ≤ 0.68) has been measured at the Canadian Synchrotron Radiation Facility. It was shown that the S K-edge in MgS was formed by the multiple scattering of the photoelectron wave within a cluster of large size (containing 27 atoms and having radius about 4.5 Å). Comparison of experimental data with theoretical results allows study of the electronic structure of this system. The analysis of partial electronic density of s-, p- and d-states makes it possible to investigate the mutual influence of sulfur s-, p- and metal d- states in the conduction band. The study of changes in experimental S K-edges XANES of Mg1-x
Fe
x
S solid solution with variation of relative Fe-Mg concentration allows the extraction of the hypothetical cubic phase (B1) of FeS, and this is supported by theoretical simulation.
Development of a new in-laboratory XAFS apparatus based on new concept
Authors: Taguchi Takeyoshi , Harada Jimpei , Kiku Atsunori , Tohji Kazuyuki , Shinoda Kozo
Published: July 2002

In a conventional in-laboratory XAFS apparatus using conventional X-ray source, sealed tube or rotating anode, has been used. In which the X-ray source is fixed and the sample is moved (translated and rotated). Hence it has been difficult or required a complex method in order to put a heavy element, such as a cryogenic cooler, high temperature furnace and an in-situ reacting cell, at a sample position. Nowadays, there is a strong demand for obtaining dynamic information of a sample and in-situ observation becomes almost unavoidable. We have developed a compact X-ray tube and a new goniometer on which X-ray source is moved and monochromatic X-ray comes out of goniometer is fixed. Therefore it becomes easier to put a various cell at a sample position.
Local structure probes of nanoscale heterogeneity in crystalline materials
Authors: Conradson Steven , Espinosa-Faller Francisco , Villella Phillip
Published: July 2002

In the conventional model of condensed matter increasing numbers of defects break down the order and ultimately convert perfect periodic crystals into aperiodic glasses. Local structure probes of a variety of materials with non-stoichiometric compositions, multiple degenerate ordering modes, or other symmetry breaking factors identify multiple ordered arrangements of atoms that render the materials heterogeneous on the nanometer scale. While exerting apparently negligible effects on bulk properties, this heterogeneity or phase separation does influence correlated or collective properties such as magnetism and phase stability.
Software based digital signal processing and spectrum deconvolution in X-ray spectroscopy
Authors: Meyer Dirk C. , Eichler Sandro , Richter Kurt , Paufler Peter
Published: July 2002

Approaches for software based digital signal processing and numerical deconvolution of measured signals which overcome limitations of state-of-the-art systems are described. The basic technical equipment for digital signal processing consists of an energy resolving detector with a preamplifier followed by a fast sampling analogue-to-digital converter (ADC). The main idea is the numerical decomposition of the measured signal into contributions caused by single photon absorption using standard pulses. The latter can be obtained by measurements under definite conditions. The maximum pulse rate is then limited only by the ratio of sampling time to the time between two pulses which should be attributed to single events. Thus pulse overlaps do not require pulse rejection. At sampling rates of 108 samples per second theoretically a comparable photon rate can be detected at throughputs of 100%. Beyond that it is outlined that in a comparable manner a numerical deconvolution of measured energy spectra (statistic distribution functions of single events) into combinations of standard spectra, which can likewise be determined by measurement, offers outstanding possibilities, too. On the one hand the energy resolution attainable for individual events for a given detector can be improved drastically by the statistical treatment of spectra. On the other hand an energy resolving work principle becomes possible for certain detectors, which do not permit this conventionally due to their poor signal to noise ratio.
EXAFS studies of americium(III)–benzimidazole complex in ethanol
Authors: Yaita T. , Tachimori S. , Edelstein N. M. , Bucher J. J. , Rao L. , Shuh D. K. , Allen P. G.
Published: July 2002

The local structures of Am, Nd and Er-Benzimidazole (Biz) in solution were determined by EXAFS. The BIZ molecule coordinated to Am and Nd through two nitrogen atoms in a bidentate fashion. Two nitrogen atoms of BIZ ligated to Am and Nd with the bond distances RAm-N = 2.63 Å and RNd-N = 2.65 Å, respectively. The total coordination number of the Am BIZ complexes (at a molar ratio of metal ion to ligand of 1:20) was ~10 but that of Nd BIZ complex was ~9.
NEXAFS multiple scattering calculations of KO2
Authors: Pedio M. , Wu Z. Y. , Benfatto M. , Mascaraque A. , Michel E. , Crotti C. , Peloi M. , Comicioli C.
Published: July 2002

Since many years the oxidation of alkali metals has being attracted much interest due to the catalytic properties of metal promoters and the simple electronic structure of alkali atoms. The alkali-oxides phase diagram indicates that the interaction of oxygen with alkali metals can lead to the formation of different atomic O2- ions and molecular O2
- and O2
2- ions. Potassium superoxide has been prepared in situ and high resolution O k-edge absorption NEXAFS spectra have been measured at the VUV beam-line at ELETTRA facility. The experimental data have been analyzed by multiple scattering approach deriving many geometrical and electronic details. In particular, we have found that the growth material structure is of the KO2 type with an O-O distance of about 1.35Å and that the transition involving single π molecular empty state of the superoxide O2
- anion has a fine structure. Multiple Scattering self consistent calculation indicates that the bond between oxygen anion and K atom is totally ionic and that the fine structure is essentially due to solid state effects.
Mn K-edge XANES spectra of manganites measured by K
β emission
Authors: García J. , Sánchez M. C. , Subías G. , Blasco J. , Proietti M. G.
Published: July 2002

The electronic state of Mn atoms in mixed valence manganites has been studied by means of X-ray absorption spectroscopy at the Mn K-edge. Higher resolution than in conventional measurements has been achieved by measuring the Mn Kβ fluorescence line. We have found a unique resonance at the edge in the XANES spectra of intermediate composition RE1−xCaxMnO3 samples. The features of these XANES spectra do not depend on small changes in the local structure around the Mn atom. However, the spectra of the intermediate composition samples can not be reproduced by a linear combination of REMnO3 and CaMnO3 spectra. Accordingly, the electronic state of Mn atoms in these compounds can not be considered as a mixture of Mn3+ and Mn4+ pure states.