bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen-Bond Distances to Halide Ions in Organic and Organometallic Crystal Structures: Up-to-date Database Study
Authors: Steiner T.
Published: July 2002

Geometrical data on hydrogen bonds to halide ions are compiled from the currently available crystal structures. Hydrogen bonds from 25 donor types to fluoride, chloride, bromide and iodide ions are considered. Compared with earlier compilations, the increased data volume allows a finer subdivision of O—H and N—H donors, and the donors C—H, S—H and P—H can be included. For a given donor type, the hydrogen-bond distance typically increases by over 0.5 Å from fluoride to chloride, 0.15 Å from chloride to bromide and 0.25 Å from bromide to iodide acceptors. The strongest of the C—H donors considered, chloroform, forms hydrogen bonds with chloride ions with an average H...Cl separation of only 2.39 Å and an average C...Cl separation of 3.42 Å. The lengthening of the N—H covalent bond in hydrogen bonds to chloride ions is quantified from neutron diffraction data.
Atomic Structure of PbZrO3 Determined by Pulsed Neutron Diffraction
Authors: Teslic S. , Egami T.
Published: July 2002

The atomic structure of lead zirconate, PbZrO3 (PZ), was studied using Rietveld refinement and atomic pair distribution function analysis of pulsed neutron powder diffraction data for the antiferroelectric, intermediate and paraelectric phases. The symmetry of PZ at T = 20 K in the antiferroelectric phase was determined to be Pbam. The structure was characterized by distortions of the ZrO6 octahedra which are smaller than in previous studies. Locally correlated displacements of Pb in the c direction develop with increasing temperature. The average magnitude was 0.06 Å at room temperature, 0.14 Å at T = 473 K and 0.20 Å in the intermediate phase at T = 508 K. The intermediate phase was characterized by in-plane antiferroelectric Pb displacements which produce 1\over 2{110} superlattice diffraction peaks. Above 473 K the local structure of PZ remains largely unchanged, in spite of the transitions in the long-range order from the antiferroelectric to the intermediate and to the paraelectric phases.
Crystal-to-Crystal Diastereoselective Transformation of 2,4,6-Triisopropyl-4'-(S)-phenylalaninocarbonylbenzophenone Methyl Ester
Authors: Hosomi H. , Ito Y. , Ohba S.
Published: July 2002

Dissymmetry of the photoproduct was induced by using a chiral substituent, (S)-methylphenylalanine, in the title compound {N-4-(2,4,6-triisopropylbenzoyl)benzoyl]-(S)-phenylalanine methyl ester (I)}. On irradiation with light from a 250 W ultra-high-pressure Hg lamp for 7 h through a long-pass filter, the photoreaction in a crystal was 100% complete without the loss of crystallinity. The crystal structures (I), before, and (II) {N-[4-(7-hydroxy-3,5-diisopropyl-8,8-dimethylbicyclo[4.2.0]octa-1,3,5-trien-7-yl)benzoyl]-(S)-phenylalanine methyl ester}, after photocyclization, have been determined by X-ray diffraction. For comparison, a crystal structure analysis has also been carried out for the photoproduct (III) of the 3′-COOMe derivative after recrystallization {methyl 3-(7-hydroxy-3,5-diisopropyl-8,8-dimethylbicyclo[4.2.0]octa-1,3,5-trien-7-yl)benzoate}. The dihedral angle between the central carbonyl plane and the triisopropylphenyl ring deviates from 90° by 10 (1)° in (I), which makes an imbalance in the intramolecular O(carbonyl)...H(methine) distances of the isopropyl groups at positions 2 and 6. The crystal structure of (II) indicates that the nearer methine H was predominantly abstracted by the carbonyl O atom in the reaction. The absolute configuration around the asymmetric C atom in the cyclobutenol ring of the product is S.
Hydrogen-bonding interactions in the crystalline-phase structures of cinnamic acid derivatives
Authors: Pálinkó I.
Published: July 2002

Secondary interactions responsible for the crystalline-phase structures of various cinnamic acids and cinnamic acid esters drawn from the Cambridge Structural Database were studied with the help of the Cerius package implemented on an SGI workstation. Primarily hydrogen-bonding interactions were sought, but deviation from planarity was also measured. For the acids, the main structural feature is the strong hydrogen bonding between the carboxyl groups. The dimers are interconnected by C—H...O intermolecular hydrogen bonds. In most cases the C atom of the C—H unit was a member of the aromatic ring. Intramolecular (olefinic) C—H...O bonds were found to be frequent, fixing synperiplanar and antiperiplanar C=C—C=O conformations with about the same abundance in the acids and exclusively synperiplanar conformations in the esters. The carbonyl group of the ester is always involved in C—H...O hydrogen bonding. Here, the C atom of the C—H unit was either a member of the aromatic ring or the olefinic group, or was attached to the alcoholic O atom of the ester group. The β-phenyl and the carboxyl or the ester groups are almost coplanar. The crystals have a layered structure and in the most frequent parallel arrangement the phenyl groups are offset by varing amounts (but always to a small extent) in neighbouring layers. The common hydrogen bonds are mostly within a layer.
Iodo-oxyapatite, the first example from a new class of modulated apatites
Authors: Alberius Henning Peter , Lidin Sven , Petříček Vačlav
Published: July 2002

Iodo-oxyapatite [pentadecacalcium iodide oxide nonaphosphate, Ca15(PO4)9IO] was synthesized by a flux method and the structure was solved from single-crystal X-ray data. The crystal structure was refined in the space group P63/m [a = 9.567 (1), c = 20.754 (2) Å and Z = 2] to wR on F of 0.0459. Iodo-oxyapatite has a typical hexagonal apatite structure but the unit cell is tripled along the hexad owing to ordering of the iodide and oxide ions along this direction.
Structure determination of lithium chloroacetate, lithium bromoacetate and lithium iodoacetate by powder diffraction
Authors: Ehrenberg H. , Hasse B. , Schwarz K. , Epple M.
Published: July 2002

Most halogenoacetates of alkali salts readily undergo a thermally induced polymerization reaction to poly-(hydroxyacetic acid) in the solid state. The lithium salts represent a remarkable exception. The crystal structures of lithium chloroacetate, lithium bromoacetate and lithium iodoacetate were determined ab initio from synchrotron powder diffraction data. The three compounds are isostructural and differ considerably from the structures of sodium chloroacetate and silver chloroacetate, two compounds that undergo polymerization. Most likely, the strong polarizing effect of the small lithium cation is responsible for the unfavorable crystal structure in which each lithium cation is coordinated to four O atoms from four different halogenoacetate molecules. Lithium chloroacetate: a = 9.3882 (9), b = 4.8452 (4), c = 9.0119 (7) Å, β = 94.330 (5)°; lithium bromoacetate: a = 9.7165 (11), b = 4.8610 (6), c = 9.0228 (11) Å, β = 93.946 (5)°; lithium iodoacetate: a = 10.1812 (10), b = 4.8922 (8), c = 9.0468 (10) Å, β = 93.251 (5)°, all crystallizing in space group P21/c with Z = 4.
Structural metrics relationships in covalently bonded organic azides
Authors: Tchertanov Luba
Published: July 2002

Geometrical parameters of covalently bonded organic azides have been analysed using X-ray structural data retrieved from the Cambridge Structural Database. The RNNN fragment geometry shows some important general features: (i) a preference for a trans
C

s
configuration; (ii) bending of the N—N—N unit; (iii) substantially different N—N bond lengths in the azide group. Electron-density redistribution within the covalently bonded azide group (relative to that in the isolated azide anion) promotes the capacity of the terminal azide N atom to form hydrogen bonds.
Order–disorder phenomena determined by high-resolution powder diffraction: the structures of tetrakis(trimethylsilyl)methane C[Si(CH3)3]4 and tetrakis(trimethylsilyl)silane Si[Si(CH3)3]4
Authors: Dinnebier Robert E. , Dollase Wayne A. , Helluy Xavier , Kümmerlen Jörg , Sebald Angelika , Schmidt Martin U. , Pagola Silvina , Stephens Peter W. , van Smaalen Sander
Published: July 2002

The compounds tetrakis(trimethylsilyl)methane C[Si(CH3)3]4 (TC) and tetrakis(trimethylsilyl)silane Si[Si(CH3)3]4 (TSi) have crystal structures with the molecules in a cubic closed-packed (c.c.p.) stacking. At room temperature both structures have space group Fm{\bar 3}m (Z = 4) with a = 13.5218 (1) Å, V = 2472.3 (1) Å3 for TSi, and a = 12.8902 (2) Å, V = 2141.8 (1) Å3 for TC. X-ray scattering data can be described by a molecule with approximately sixfold orientational disorder, ruling out a structure with free rotating molecules. Upon cooling, TSi exhibits a first-order phase transition at T

c
= 225 K, as is characterized by a jump of the lattice parameter of Δa = 0.182 Å and by an exothermal maximum in differential scanning calorimetry (DSC) with ΔH = 11.7 kJ mol−1 and ΔS = 50.0 J mol−1 K−1. The structure of the low-temperature phase is refined against X-ray powder data measured at 200 K. It has space group P2
13 (Z = 4), a = 13.17158 (6) Å and V = 2285.15 (2) Å3. The molecules are found to be ordered as a result of steric interactions between neighboring molecules, as is shown by analyzing distances between atoms and by calculations of the lattice energy in dependence on the orientations of the molecules. TC has a phase transition at T

c1 = 268 K, with Δa
1 = 0.065 Å, ΔH
1 = 3.63 kJ mol−1 and ΔS
1 = 13.0 J mol−1 K−1. A second first-order phase transition occurs at T

c2 = 225 K, characterized by Δa
2 = 0.073 Å, ΔH
2 = 6.9 kJ mol−1 and ΔS
2 = 30.0 J mol−1 K−1. The phase transition at higher temperature has not been reported previously. New NMR experiments show a small anomaly in the temperature dependence of the peak positions in NMR to occur at T

c2. Rietveld refinements were performed for the low-temperature phase measured at T = 150 K [space group P2
13, lattice parameter a = 12.609 (3) Å], and for the intermediate phase measured at T = 260 K [space group Pa{\bar 3}, lattice parameter a = 12.7876 (1) Å]. The low-temperature phase of TC is formed isostructural to the low-temperature phase of TSi. In the intermediate phase the molecules exhibit a twofold orientational disorder.
The performances of neutron collimators. I. Accurate transmitted intensity evaluations for neutron collimator systems
Authors: Rossitto F. , Poletti G.
Published: July 2002

Limitations imposed by the geometry of Soller collimator systems on luminosity and resolution of neutron diffraction equipment are studied on the grounds of angular and spatial distribution of neutrons. Transmission functions for collimator systems of arbitrary complexity are derived. The influence of the mutual distances among the various components of the experimental set-up on the shape of transmission functions is given in evidence. Careful intensity measurements performed with well diversified arrangements of Soller collimators are in fair agreement with our theoretical results. The way to improve the performances of neutron diffraction equipment by a proper choice of all the geometrical parameters is shown.
The atom–atom approximation and the lattice energies of 2,2'-bis-1,3-dithiole (TTF), 7,7,8,8-tetracyanoquinodimethane (TCNQ) and their 1:1 complex (TTF–TCNQ)
Authors: Govers H. A. J.
Published: July 2002

The van der Waals and repulsive contributions to the lattice energies of TTF (C6H4S4), TCNQ (C12H4N4) and TTF-TCNQ (C6H4S4.C12H4N4) at room temperature were calculated by the atom-atom approximation. In addition the Madelung electrostatic contributions were calculated by Ewald's method for TTF and TCNQ. The combined atom-atom and electrostatic contributions produced lattice energies in accordance with the experimental enthalpies of sublimation and dissociation within 0-5 kcal mol-1.
Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus
Authors: Mancini Erika J. , Fuller Stephen D.
Published: July 2002

The recent advances in the resolution obtained by single-particle reconstructions from cryo-electron microscopy (cryo-EM) have led to an increase in studies that combine X-ray crystallographic results with those of electron microscopy (EM). Here, such a combination is described in the determination of the structure of an enveloped animal virus, Semliki Forest virus, at 9 Å resolution. The issues of model bias in determination of the structure, the definition of resolution in a single-particle reconstruction, the effect of the correction of the contrast-transfer function on the structure determined and the use of a high-resolution structure of a subunit in the interpretation of the structure of the complex are addressed.
Structure of Azurin I from the Denitrifying Bacterium Alcaligenes xylosoxidans NCIMB 11015 at 2.45 Å Resolution
Authors: Li Chunmin , Inoue Tsuyoshi , Gotowda Masaharu , Suzuki Shinichiro , Yamaguchi Kazuya , Kataoka Kunishige , Kai Yasushi
Published: July 2002

Azurin I from Alcaligenes xylosoxidans NCIMB 11015 (AzN-I) was crystallized by using PEG 4000 as a precipitant. The crystals belong to the monoclinic crystal system and have a space group C2 with the unit-cell parameters of a = 130.67, b = 54.26, c = 74.55 Å, and β = 95.99°. The structure of AzN-I has been solved by the molecular replacement method. Azurin II from the same bacterium (AzN-II) was chosen as the initial structural model. The final crystallographic R value is 17.3% and free R value is 23.6% for 10 958 reflections at a resolution of 2.45 Å. The root-mean-square deviations for main-chain atoms range between 0.19 and 0.26 Å among the four independent molecules in the asymmetric unit. The Cu atom is coordinated to Nδ of His46 and His117 at 2.0 (1) and 1.9 (1) Å, and to Sγ of Cys112 at 2.2 (1) Å, while the carbonyl O atom of Gly45 and Sδ of Met121 coordinate axially to Cu atom at 2.5 (1) and 3.1 (1) Å, respectively. The Cu—N and Cu—S distances of AzN-I are quite similar to those of AzN-II, however, the Cu—O (Gly45) bond length in AzN-I is 0.25 Å shorter than its counterpart in AzN-II. The results have been used to discuss the differences in the spectra of these two proteins.
The Two-Dimensional Histogram as a Constraint for Protein Phase Improvement
Authors: Goldstein Alexandra , Zhang Kam Y. J.
Published: July 2002

The joint distribution of electron density and its gradient in a protein electron-density map was examined. This joint distribution was represented by a two-dimensional histogram (2D histogram) of electron-density values and the modulus of the gradient. 16 structures representing distinct protein-fold families were selected to study the dependence of the 2D histogram on resolution, overall temperature factor, structural conformation and phase error. The similarity between the histograms for a pair of structures was measured by correlation coefficient, and the residual provided a measure of the difference. The 2D histogram was found to vary with resolution and overall temperature factor, but was found to be insensitive to structure conformation. The average correlation coefficient between pairs of 2D histograms at three different resolutions examined was 0.90 with a standard deviation of 0.04. The average residual for the same condition was 0.13 with a standard deviation of 0.03. The 2D histogram was also found to be sensitive to phase error. The average correlation coefficient and residual between 2D histograms with 10° phase difference are 0.71 and 0.18, respectively. The variation of the 2D histogram resulting from structure-conformation changes was estimated to be equivalent to that of a 4° phase error. This establishes the minimal phase error that a 2D histogram-matching method could achieve. The conservation of the 2D histogram with respect to structure conformation enables the prediction of the ideal 2D histogram for unknown structures. The sensitivity of the 2D histogram to phase error suggests that it could be used as a target for the density-modification method and also could be used as a figure of merit for phase selection in ab initio phasing.
Crystallization and preliminary X-ray studies of the Rhizobium meliloti DctD two-component receiver domain
Authors: Staley Mark , Zeringue Lori C. , Kidd Richard D. , Nixon B. Tracy , Farber Gregory K.
Published: July 2002

The Rhizobium meliloti DctD two-component receiver domain was expressed in Escherichia coli and purified to homogeneity. Crystals were obtained using the hanging-drop vapor-diffusion geometry with ammonium phosphate as the precipitant. The crystals diffract to 2.3 Å and exhibit the symmetry of space group I222 or I212121. The unit-cell dimensions are a = 59.0, b = 58.6 and c = 169.8 Å. The asymmetric unit contains a dimer and the crystals have a Vm
of 2.16 Å3 Da−1.
Crystallization and preliminary X-ray diffraction studies of 6-phosphogluconate dehydrogenase from Lactococcus lactis
Authors: Tetaud E. , Hall D. R. , Gourley D. G. , Leonard G. A. , Arkison S. , Barrett M. P. , Hunter W. N.
Published: July 2002

6-Phosphogluconate dehydrogenase is one of the seven enzymes involved in the pentose phosphate pathway. Crystals of a mammalian and a protozoan enzyme have been obtained previously and structures determined. It is reported here that a bacterial 6-phosphogluconate dehydrogenase, from Lactococcus lactis, has been purified and used in crystallization trials. Large prisms suitable for a detailed structural analysis have been obtained and characterized as orthorhombic, space group F222, with a = 70.4, b = 105.7, c = 474.6 Å. Diffraction has been observed to 2.2 Å resolution using synchrotron radiation. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure–activity relationships of this enzyme.
Crystallization and preliminary crystallographic analysis of the archaeal intron-encoded endonuclease I-DmoI
Authors: Dalgaard Jacob Z. , Silva George H. , Belfort Marlene , Van Roey Patrick
Published: July 2002

Two forms of the archaeal intron-encoded site-specific endonuclease I-DmoI, namely I-DmoIc and I-DmoIl, have been purified and crystallized. Crystals of I-DmoIc are rod-shaped and diffract to 3.0 Å resolution, but further analysis was hampered by twinning. Crystals of I-DmoIl, which is a six-amino-acid C-terminal truncation of I-DmoIc, are plate shaped and belong to space group C2 with cell parameters a = 93.72, b = 37.03, c = 55.56 Å, β = 113.4°, with one molecule per asymmetric unit (Vm
= 2.01 Å3 Da−1). The crystals diffract to at least 2.3 Å resolution. A complete native data set has been measured and structure determination is on-going.
HAD, a Data Bank of Heavy-Atom Binding Sites in Protein Crystals: a Resource for Use in Multiple Isomorphous Replacement and Anomalous Scattering
Authors: Islam Suhail A. , Carvin David , Sternberg Michael J. E. , Blundell Tom L.
Published: July 2002

Information on the preparation and characterization of heavy-atom derivatives of protein crystals has been collected, either from the literature or directly from protein crystallographers, and assembled in the form of a heavy-atom data bank (HAD). The data bank contains coordinate data for the heavy-atom positions in a form that is compatible with the crystallographic data in the Brookhaven Protein Data Bank, together with a wealth of information on the crystallization conditions, the nature of the heavy-atom reagent and references to relevant publications. Some statistical information derived from the data bank, such as the most popular heavy-atom derivatives, is also included. The information can be directly accessed and should be useful to protein crystallographers seeking to improve their success in preparing heavy-atom derivatives for the methods of isomorphous replacement and anomalous dispersion. The World Wide Web address of HAD is http://www.icnet.uk/bmm/had.
Crystallization and preliminary diffraction data of neurotoxin Ts-γ from the venom of the scorpion Tityus serrulatus
Authors: Golubev A. M. , Lee W.-H. , Marangoni S. , Novello J. C. , Oliveira B. , Toyama M. H. , Polikarpov I.
Published: July 2002

Scorpion neurotoxin Ts-γ was isolated from Tityus serrulatus venom and purified to apparent homogeneity by ion-exchange HPLC. Crystals of the toxin were grown using polyethylene glycol 6000 as precipitant and were found to belong to the monoclinic space group P21 with cell parameters a = 22.20, b = 36.90, c = 31.57 Å, β = 100.85°. The crystals diffract beyond 1.73 Å resolution at a synchrotron beamline, being notably stable during X-ray exposure. The structure has been solved by molecular replacement using the very high resolution structure of Sahara scorpion Androctonus australis Hector (PDB code 1AHO) as a search model.
Crystallization and preliminary X-ray studies of the basic lectin from the seeds of Artocarpus hirsuta
Authors: Rao K. N. , Gurjar Madhura M. , Gaikwad Sushama M. , Khan M. Islam , Suresh C. G.
Published: July 2002

The basic lectin from Artocarpus hirsuta specific towards methyl α-galactose has been purified and crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitant. Three different crystal forms, orthorhombic I, orthorhombic II and hexagonal, were grown under the same crystallization conditions. The orthorhombic forms belonged to space group P212121 with unit-cell dimensions a = 92.9, b = 99.8, c = 166.2 Å and a = 89.9, b = 121.9, c = 131.6 Å, respectively. The unit-cell dimensions of the hexagonal form were a = b = 84.1 and c = 271.7 Å and the space group was P6122.
Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 Å resolution
Authors: Wood Stephen D. , Wright Lisa M. , Reynolds Colin D. , Rizkallah Pierre J. , Allen Anthony K. , Peumans Willy J. , Van Damme Els J. M.
Published: July 2002

The X-ray crystal structure of native Scilla campanulata agglutinin, a mannose-specific lectin from bluebell bulbs and a member of the Liliaceae family, has been determined by molecular replacement and refined to an R value of 0.186 at 1.7 Å resolution. The lectin crystallizes in space group P21212 with unit-cell parameters a = 70.42, b = 92.95, c = 46.64 Å. The unit cell contains eight protein molecules of Mr
= 13143 Da (119 amino-acid residues). The asymmetric unit comprises two chemically identical molecules, A and B, related by a non-crystallographic twofold axis perpendicular to c. This dimer further associates by crystallographic twofold symmetry to form a tetramer. The fold of the polypeptide backbone closely resembles that found in the lectins from Galanthus nivalis (snowdrop) and Hippeastrum (amaryllis) and contains a threefold symmetric β-prism made up of three antiparallel four-stranded β-sheets. Each of the four-stranded β-sheets (I, II and III) possesses a potential saccharide-binding site containing conserved residues; however, site II has two mutations relative to sites I and III which may prevent ligation at this site. Our study provides the first accurate and detailed description of a native (unligated) structure from this superfamily of mannose-specific bulb lectins and will allow comparisons with a number of lectin–saccharide complexes which have already been determined or are currently under investigation.
Crystallization and preliminary X-ray analysis of human rhinovirus serotype 2 (HRV2)
Authors: Verdaguer Núria , Marlovits Thomas C. , Bravo Jerónimo , Stuart David I. , Blaas Dieter , Fita Ignacio
Published: July 2002

Human rhinoviruses, the major cause of mild recurrent infections of the upper respiratory tract, are small icosahedral particles. Over 100 different serotypes have been identified. The majority (91 serotypes) use intercellular adhesion molecule 1 as the cell-attachment site; ten serotypes (the minor group) bind to members of the low-density lipoprotein receptor. Three different crystal forms of the minor-group human rhinovirus serotype 2 (HRV2) were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium/potassium phosphate as precipitants. Monoclinic crystals, space group P21, diffracted at least to 2.8 Å resolution, and two complete virus particles were located in the crystal asymmetric unit. A second type of crystals had a compact cubic like morphology and diffracted beyond 2.5 Å resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 309.3, b = 353.5, c = 759.6 Å, and contain one virus particle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 308.7, b = 352.2, c = 380.5 Å, diffracted to high resolution (beyond 1.8 Å) and contained 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral particle's dyad axes.
Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli
Authors: Blackwell Nicholas C. , Cullis Paul M. , Cooper Ronald A. , Izard Tina
Published: July 2002

2-Dehydro-3-deoxygalactarate (DDG) aldolase (E.C. 4.1.2.20) catalyzes the reversible aldol cleavage of DDG and 2-dehydro-3-deoxyglucarate to pyruvate and tartronic semialdehyde. Rhombohedral crystals of recombinant DDG aldolase from Escherichia coli K-12 were obtained. The crystals belong to space group R32 with unit-cell parameters a = 93 Å, α = 85°. The crystals diffract to beyond 1.8 Å resolution on a Cu Kα rotating-anode generator. The asymmetric unit is likely to contain two molecules, corresponding to a packing density of 1.34 Å3 Da−1.
Macromolecular crystallography with a third-generation synchrotron source
Authors: Lindley Peter F.
Published: July 2002

The European Synchrotron Radiation Facility (ESRF) at Grenoble, France, is a 6 GeV machine producing hard X-radiation that can be used for pure and applied research in a wide range of disciplines including physics, chemistry, structural biology, materials science, the earth sciences, engineering and medicine. The overall nature of the machine will be described, including the features that give rise to the notation `third-generation source'. The ESRF is equipped with a number of beamlines which can be used for macromolecular crystallography. Applications include the use of very small crystals, large unit cells, data collection at high resolution, anomalous dispersion measurements for phase determination and time-resolved studies. Key features of these applications will be described.
New processing tools for weak and/or spatially overlapped macromolecular diffraction patterns
Authors: Bourgeois Dominique
Published: July 2002

Tools originally developed for the treatment of weak and/or spatially overlapped time-resolved Laue patterns were extended to improve the processing of difficult monochromatic data sets. The integration program PrOW allows deconvolution of spatially overlapped spots which are usually rejected by standard packages. By using dynamically adjusted profile-fitting areas, a carefully built library of reference spots and interpolation of reference profiles, this program also provides a more accurate evaluation of weak spots. In addition, by using Wilson statistics, it allows rejection of non-redundant strong outliers such as zingers, which otherwise may badly corrupt the data. A weighting method for optimizing structure-factor amplitude differences, based on Bayesian statistics and originally applied to low signal-to-noise ratio time-resolved Laue data, is also shown to significantly improve other types of subtle amplitude differences, such as anomalous differences.
Detecting outliers in non-redundant diffraction data
Authors: Read Randy J.
Published: July 2002

Outliers are observations which are very unlikely to be correct, as judged by independent observations or other prior information. Such unexpected observations are treated, effectively, as being more informative about possible models, so they can seriously impede the course of structure determination and refinement. The best way to detect and eliminate outliers is to collect highly redundant data, but it is not always possible to make multiple measurements of every reflection. For non-redundant data, the prior expectation given either by a Wilson distribution of intensities or model-based structure-factor probability distributions can be used to detect outliers. This captures mostly the excessively strong reflections, which dominate the features of electron-density maps or, even more so, Patterson maps. The outlier rejection tests have been implemented in a program, Outliar.
Crystallization of truncated human apolipoprotein A-I in a novel conformation
Authors: Borhani David W. , Engler Jeffrey A. , Brouillette Christie G.
Published: July 2002

The crystallization of recombinant human apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, in a new crystal form 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, in the presence of β-D-octylglucopyranoside, in space group I222 or I212121, with unit-cell parameters a = 37.11, b = 123.62, c = 164.65 Å and a diffraction limit of 3.2 Å. These form II crystals grow under conditions of significantly lower ionic strength than the original form I crystals (space group P212121, a = 97.47, b = 113.87, c = 196.19 Å, diffraction limit 3.0 Å). Packing arguments show that the unusual open conformation of apo Δ(1–43)A-I found in the form I crystals cannot be packed into the smaller oddly proportioned form II unit cell. Monomeric apo Δ(1–43)A-I, as either a four-helix bundle (∼75 × 30 × 30 Å) or an extended helical rod (∼150 × 20 × 20 Å), can be packed into the form II unit cell. It is concluded, therefore, that apo Δ(1–43)A-I may have crystallized in one of these distinct conformations in the form II crystals.
Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13
Authors: Perrakis Anastassis , Cipriani Florent , Castagna Jean-Charles , Claustre Laurent , Burghammer Manfred , Riekel Christian , Cusack Stephen
Published: July 2002

There is a growing demand for the examination of protein microcrystals at third-generation synchrotron sources. After successful pilot experiments at EMBL/ESRF, which proved that protein microcrystals are often suitable for data collection, operation of the microfocus beamline ID13 was made more user-friendly and suitable for macromolecular crystallography experiments. Given the excellent quality of the beamline microfocusing optics, the key element for successful experiments becomes the handling and visualization of microcrystals. To address this, a microdiffractometer has been designed to allow maximum precision combined with ease of usage and is currently under construction.
The finer things in X-ray diffraction data collection
Authors: Pflugrath J. W.
Published: July 2002

X-ray diffraction images from two-dimensional position-sensitive detectors can be characterized as thick or thin, depending on whether the rotation-angle increment per image is greater than or less than the crystal mosaicity, respectively. The expectations and consequences of the processing of thick and thin images in terms of spatial overlap, saturated pixels, X-ray background and I/σ(I) are discussed. The d*TREK software suite for processing diffraction images is briefly introduced, and results from d*TREK are compared with those from another popular package.
Crystallization and preliminary X-ray diffraction studies of human catalase
Authors: Nagem R. A. P. , Martins E. A. L. , Gonçalves V. M. , Aparício R. , Polikarpov I.
Published: July 2002

The enzyme catalase (H2O2–H2O2 oxidoreductase; E.C. 11.1.6) was purified from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 Å resolution. The enzyme crystallized in the space group P212121, with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 Å. A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.
Crystallization and preliminary X-ray diffraction studies of a Bowman–Birk inhibitor from Vigna unguiculata seeds
Authors: Rao K. N. , Hegde S. S. , Lewis R. J. , Suresh C. G.
Published: July 2002

A Bowman–Birk type trypsin/chymotrypsin inhibitor isolated from Vigna unguiculata seeds has been crystallized. Crystals were grown using the vapour-diffusion method at pH 4.0 using citrate/phosphate as a buffer and 30% saturated ammonium sulfate as precipitant. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 32.4, b = 61.8, c = 32.9 Å, β = 114.5°. The Matthews coefficient calculated assuming two molecules in the asymmetric unit was 1.95 Å3 Da−1, which corresponds to a 37% solvent content. X-ray data were collected to 2.5 Å resolution from a flash-frozen crystal. The structure was solved using the molecular-replacement method using tracy soybean inhibitor structure (PDB entry 1pi2) as a model.
Experiences with CCD detectors on a home X-ray source
Authors: Muchmore Steven W.
Published: July 2002

Charged-coupled device (CCD) detectors have been widely accepted as detectors for collecting X-ray diffraction images. The CCD detector offers a sensitive detection system well suited for diffraction analysis and, compared with other detectors on the market, a relatively rapid system for read-out of the collected image. The two predominant markets for the CCD detector have been those in which relatively short exposure times are used, i.e. small-molecule X-ray diffraction and large-molecule crystallography at high-intensity synchrotron sources. CCD detectors have not been commonly used on rotating-anode X-ray sources for large-molecule crystallography. Comparison of the performance of the CCD detectors with commercially available image-plate detectors shows that the CCD detectors function in a similar fashion to image-plate-based detectors.
Structural studies of the Msx-1 homeodomain–DNA complex I
Authors: DeWees Stacy , Geiger James H.
Published: July 2002

Crystals of the Msx-1 homeodomain–DNA complex have been obtained by hanging-drop vapor diffusion at 293 K in 12% PEG 4000 and 0.1 M sodium acetate pH 4.6. The homeodomain consists of 60 amino acids and is the DNA-binding domain. The DNA in the complex was 16 base pairs with the sequence 5′-TGTCACTAATTGAAGG-3′, containing an overhang T at each end. The crystals diffract to 2.15 Å (99.8% completeness) using cryogenic (123 K) conditions. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 33.66, b = 60.96, c = 83.37 Å. The structure will illuminate the details of Msx-1–DNA binding specificity and clarify its role in transcriptional regulation. Mutations in Msx-1 cause craniofacial deformities in mice.
Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data
Authors: Darkes Malcolm J. M. , Bradshaw Jeremy P.
Published: July 2002

Neutron-diffraction data were collected from stacked bilayers of 1,2-dioleoyl-sn-glycero-phosphocholine under conditions of increasing relative humidity at both 0 and 8.06% 2H2O. Over the period of data collection, the d-repeat of both swelling-series samples increased. Each family of structure factors, representing each of the five orders of diffraction, are shown to lie on smooth curves, allowing structure factors of intermediate d-repeat to be determined. In the case of the 8.06% 2H2O data, but not the 0% 2H2O data, all observed structure factors lie on a single continuous transform. 8.06% 2H2O has a net neutron-scattering density of zero; its use in neutron-diffraction experiments presents a novel application of the so-called `minus fluid' approach, without mathematical manipulation. The data are used to demonstrate the increased accuracy inherent in this real-time swelling-series approach. A quantitative analysis of errors caused by differences in d-repeat in difference subtractions is presented.
Musings about the development of XAFS
Authors: Stern Edward A.
Published: July 2002

A personal recollection of the development of X-ray absorption fine structure (XAFS) into a structure-determination technique is presented. Because of confusion in the theoretical explanation of the `Kronig structure', now called EXAFS, the extended XAFS, its explanation remained unresolved for about 40 years. As I was introduced to the EXAFS phenomenon by Farrel Lytle and saw his impressive data, the thought came to me that scattering of the photoelectron from surrounding atoms could be the mechanism of the effect. My graduate student, Dale Sayers, agreed to work on developing the theory under my supervision and to make EXAFS measurements under Lytle's supervision as his PhD thesis. The theory led to the idea of a Fourier transform of the EXAFS, which showed peaks from surrounding atoms, proving the validity of the theory and suggesting the method of structure determination by using standards from known structures. Within a few years, facilities at synchrotron sources were developed to measure XAFS, opening up the technique to the general scientific community. In spite of some initial growing pains, XAFS has matured into a powerful technique for local structure and has been applied to obtain magnetic structure, in addition to distribution of atoms. Other related techniques have been spawned from XAFS, expanding the impact of the original phenomenon.
Time-resolved energy-dispersive XAFS study on the reduction process of Cu-ZSM-5 catalysts
Authors: Yamaguchi Aritomo , Inada Yasuhiro , Shido Takafumi , Asakura Kiyotaka , Nomura Masaharu , Iwasawa Yasuhiro
Published: July 2002

The time-resolved reduction process of copper cations in ZSM-5 during temperature-programmed reduction (300-700 K) was studied by energy dispersive X-ray absorption fine structure (DXAFS). The Cu K-edge DXAFS spectra for isolated Cu2+ species in the channels of ZSM-5 were recorded at an interval of 1 s during the reduction. The curve fitting analysis of the EXAFS data and the XANES analysis revealed that the isolated Cu2+ species in the channels were reduced stepwise. They were reduced to isolated Cu+ species at 400-450 K and the Cu+ species to Cu0 metallic clusters at 550-650 K. Small clusters like Cu4 were initially formed, followed by particle growth. A small part of them went out to the outer surfaces of ZSM-5 during the reduction.
Zirconium speciation in lactate solutions and polyacrylate gels
Authors: Rose Jérome , Chauveteau Guy , Tabary René , Renard Michel , Omari Aziz , Toulhoat Hervé
Published: July 2002

Controlling gelation kinetics is an important objective for several applications (ceramic and thin film syntheses, reduction in permeability of porous rock, etc.). There is a growing interest in studying the gelation of polymers by zirconium, a crosslinker of lower toxicity than the chromium which is still commonly used. XAS at the Zr K-edge was performed at the European Synchrotron Radiation Facility (ESRF) on the BM32 beamline. The fluorescence detection was used to carry out successful in situ speciation at concentrations as low as 36 ppm. The Zr speciation was determined both in ZrLa (where La stands for lactate) aqueous solutions and in gels of a terpolymer of acrylamide having 2% of zirconium reactive acrylate side groups and 2% of sulfonate groups introduced to prevent syneresis. XANES results show that Zr is always in a dodecahedral geometry. In ZrLa solutions, EXAFS results indicate that Zr species grow from a dimer Zr2(La)6 to a tetramer (Zr4(La)
x
) and then to larger polymers resulting from tetramer associations, as the Zr concentration decreases from 51840 ppm to 36ppm. In polymer gels, Zr species appear to be dimers at pH 6 while tetramers are found when gelation occurred at pH 7. Calculations taking into account multiple scattering effects as well as dynamic molecular calculation confirmed conclusions derived from conventional EXAFS analysis.
Statistical evaluations in fitting problems
Authors: Klementev K. V.
Published: July 2002

The problem of error analysis is considered taking into account all possible correlations and a prior information about the accessible parameter space. Special attention is paid to the correct determination of the relative weight of experimental data and the a priori guess. The applications of statistical χ2- and F-tests to the fitting problems are also discussed.
Experimental technique for radiative-process-resolved X-ray absorption spectroscopy at the inner-shell excitation thresholds
Authors: Muramatsu Yasuji , Ueno Yuko , Sasaki Teikichi A. , Gullikson Eric M. , Perera Rupert C. C.
Published: July 2002

Partial-fluorescence-yield (PFY) x-ray absorption measurements, using the optimized window widths of position sensitive detectors in wave-length dispersive x-ray spectrometers, have been applied for radiative-process-resolved (RPR) x-ray absorption spectroscopy. We have measured PFY-absorption spectra of graphite and diamond at the C K threshold and of h-BN and c-BN at the B K threshold. Resonant elastic x-ray scattering was observed in graphite and h-BN on their PFY-absorption spectra, and excitonic x-ray scattering was observed in diamond and c-BN. These results show that PFY-absorption measurements for RPR x-ray absorption spectroscopy can provide the information about the electronic structures and the radiative-decay process in inner-shell excitation.
Natural linear dichroism in pyrite (FeS2): experiments and calculations
Authors: Cabaret Delphine , Brouder Christian , Arrio Marie-Anne , Sainctavit Philippe , Joly Yves , Rogalev Andrei , Goulon José
Published: July 2002

Electric quadrupole transitions are revealed through the angular dependence of X-ray absorption spectra in a cubic crytal. Data collection was achieved at the iron K-edge in pyrite (FeS2) by using the angular moment method developed for X-ray Natural Circular Dichoism (XNCD) measurements. The natural linear dichroism (XNLD) was found to be around 0.5% of the edge jump. Experimental results are compared with monelectronic and multilectronic calculations. Calculations allow to quantitatively determine the proportion of quadrupolar transitions in the pre-edge structure and the anisotropy is explained in terms of structural and electronic parameters.
Magnetic circular dichroism at transition metal L
2,3 edges in D03-type (Fe1-x
Mn
x
)3Al alloys
Authors: Soda Kazuo , Yoshimoto Osamu , Nozaki Hiroshi , Takeuchi Tsunehiro , Mizutani Uichiro , Kato Hideaki , Kato Masaaki , Nishino Yoichi , Imada Shin , Suga Shigemasa , Matsushita Tomohiro , Saitoh Yuji
Published: July 2002

We have measured magnetic circular dichroism (MCD) spectra at the transition-metal L
2,3 edges in D03-type (Fe1-x
Mn
x
)3Al in order to investigate their local magnetic moments. The analysis of the spectra shows that Fe has moments much larger than Mn, whose moment is ferromagnetically coupled with the Fe one. This does not lend support to the antiferromagnetic mechanism proposed for the reduction in magnetization as well as a large Mn moment predicted for x = 1/3. The evolution of satellites found in the Mn spectrum with x increased suggests that the change in the electronic state may result in the magnetization reduction.
EELFS study of the cementite local atomic structure
Authors: Maratkanova A. N. , Surnin D. V. , Deev A. N. , Ruts Yu. V. , Schastlivtsev V. M. , Yakovleva I. L.
Published: July 2002

The changes in the nearest - neighbour surroundings of carbon atoms in the cementite Fe3C lattice due to the heat treatment are analysed by the Extended Energy Loss Fine Structure (EELFS) method. To study the local atomic structure of the carbon steel U15 after different heat treatment regimes the electron energy - loss spectra above the C K edge and Fe L2,3 edge were measured. The measured experimental EELFS spectra were treated by the standard for the Extended X - ray Absorption Fine Structure method procedure using Fourier transformation to obtain the parameters of the nearest - neighbour atomic surroundings. Qualitatively the assumption was made that the number of the iron atoms in the carbon atom nearest - neighbour surroundings changes due to the heat treatment, the evidence of which was the change in the ratio of the first two feature intensities of the atomic radial distribution function. This assumption is consistent well with the previous Mössbauer data.
The zinc environment in Langmuir–Blodgett phospholipid multilayers
Authors: Morante Silvia
Published: July 2002

The Zinc environment of a system formed by Langmuir-Blodgett phospholipid multi-layers is investigated by employing X-ray absorption spectroscopy. A comparative analysis of the Extended X-ray Absorption Fine Structure and Near Edge regions of the X-ray absorption spectra at the Zinc K-edge, in presence and in absence of the Myelin Basic Protein, clearly indicates that Zinc ions are bound to the heads of the phospholipidic molecules, while the presence of Myelin Basic Protein induces a visible distorsion of the geometry of the Zinc environment. These findings represent a first important step in understanding the interplay among the lipids of the myelin sheath, Myelin Basic Protein and Zinc, as Langmuir-Blodgett phospholipid multi-layers represent a valuable model for the multilamellar structure of the membrane surrounding the nerve axon.
Non-symmetric influences in the total electron yield X-ray magnetic circular dichroism signal in applied magnetic fields
Authors: Goering E. , Gold S. , Bayer A. , Schuetz G.
Published: July 2002

No abstract
Dopant structural distortions in high-temperature superconductors: an active or a passive role?
Authors: Haskel Daniel , Stern Edward A. , Dogan Fatih , Moodenbaugh Arnie R.
Published: July 2002

The parent compounds of high-temperature superconductors, such as YBa2Cu3O6 and La2CuO4, are strongly interacting electron systems, rendering them insulators with Mott–Hubbard gaps of a few electronvolts. Charge carriers (holes) are introduced by chemical doping, causing an insulator–metal (IM) transition and, at low temperatures, superconductivity. The role of dopants is widely seen as limited to the introduction of holes into the CuO2 planes (i.e. occupying electronic states derived from Cu 3d_{x^{2}-y^{2}} and O 2p

x,y
atomic orbitals). Most theories of high-T

c
superconductivity deal with pairing interactions between these planar holes. Local distortions around dopants are poorly understood, because of the experimental difficulty in obtaining such information, particularly at low doping. This has resulted in the neglect, in most theories, of the effect of such distortions on the chemical and electronic structure of high-T

c
superconductors. Angular-resolved X-ray absorption fine structure (XAFS) spectroscopy on oriented samples is an ideal technique to elucidate the dopant distortions. Element specificity, together with a large orientation dependence of the XAFS signal in these layered structures, allows the local structure around dopants to be resolved. Results are presented here on (Sr, Ba) and Ni dopants, which substitute at the La and Cu sites, respectively, of insulating La2CuO4. The relevance of the measured local distortions for a complete understanding of the normal and superconducting properties of cuprates is discussed.
Calcium L-edge XANES study of some calcium compounds
Authors: Naftel S. J. , Sham T. K. , Yiu Y. M. , Yates B. W.
Published: July 2002

The Ca L3,2-edge XANES spectra of six calcium salts have been measured in both total electron and fluorescence yields using a high-resolution spherical grating monochromator. The compounds investigated were; CaF2, CaCO3, CaCl2 ˙2H2O, calcium phosphate, calcium glycerophosphate and calcium gluconate. We find that the fine structure of the Ca L3,2-edges for each compound is unique and relates to the local structure of the Ca atom. The implications of these results to the study of the structure of calcium binding sites in systems of biologically interest will be discussed.