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Atomic Coordinates (atomic + coordinate)
Selected AbstractsMonoclinic PZN-8%PT [Pb(Zn0.3066Nb0.6133Ti0.08)O3] at 4,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2007Jennifer S. Forrester The structure of the relaxor ferroelectric Pb(Zn0.3066Nb0.6133Ti0.08)O3 (lead zinc niobium titanium trioxide), known as PZN-8%PT, was determined at 4,K from very high resolution neutron powder diffraction data. The material is known for its extraordinary piezoelectric properties, which are closely linked to the structure. Pseudo-cubic lattice parameters have led to considerable controversy over the symmetry of the structure. We find the structure to be monoclinic in the space group Cm (No. 8), with the Zn, Nb and Ti cations sharing the octahedrally coordinated B site (site symmetry m, special position 2a) and Pb occupying the 12-coordinate A site (site symmetry m, special position 2a). O atoms occupy a disorted octahedron around the B site (site symmetry m and special position 2a, and site symmetry 1 and general position 4b). Atomic coordinates have been determined for the first time, allowing the direction of spontaneous polarization to be visualized. [source] Molecular complementarity between tetracycline and the GTPase active site of elongation factor TuACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2006Susan E. Heffron Two crystal forms of a complex between trypsin-modified elongation factor Tu,MgGDP from Escherichia coli and the antibiotic tetracycline have been solved by X-ray diffraction analysis to resolutions of 2.8 and 2.1,Å, respectively. In the P21 form, cocrystals were grown from a solution mixture of the protein and tetracycline. Six copies of the trypsin-modified EF-Tu,MgGDP,tetracycline complex are arranged as three sets of dimers in the asymmetric unit. In the second crystal form, tetracycline was diffused into P43212 crystals, resulting in a monomeric complex in the asymmetric unit. Atomic coordinates have been refined to crystallographic R factors of 18.0% for the P21 form and 20.0% for the P43212 form. In both complexes, tetracycline makes significant interactions with the GTPase active site of EF-Tu. The phenoldiketone moiety of tetracycline interacts directly with the Mg2+, the ,-phosphate group of GDP and two amino acids, Thr25 and Asp80, which are conserved in the GX4GKS/T and DX2G sequence motifs found in all GTPases and many ATPases. The molecular complementarity, previously unrecognized between invariant groups present in all GTPase/ATPases and the active moiety of tetracycline, may have wide-ranging implications for all drugs containing the phenoldiketone moiety as well as for the design of new compounds targeted against a broad range of GTPases or ATPases. [source] Parametric Rietveld refinement for the evaluation of powder diffraction patterns collected as a function of pressureJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2010Ivan Halasz Under the assumption that the structural parameters of a crystalline phase change `smoothly' with increasing pressure, the evolution of the parameters can be parameterized as a function of pressure using continuous monotonic functions. Four different approaches to determine the structural evolution of As2O5 with increasing pressure from a set of powder diffraction patterns collected over the pressure range from 2.5 to 19.5,GPa have been investigated. Approach (A) was the common sequential refinement of atomic coordinates with restraints on the geometry and was compared with three parameterization approaches. Approach (B) used direct parameterization by low-order polynomials of each crystallographically distinct atomic coordinate, (C) described the atoms of the asymmetric unit as a rigid body and allowed the internal degrees of freedom of the rigid body to vary with the change in pressure using rigid unit modes, and (D) described the crystal structure as a distortion of the higher-symmetry structure of As2O5 (which is here also a high-temperature phase) by using symmetry-adapted distortion modes. Approach (D) offers the possibility to directly introduce an order parameter into Rietveld refinement through an empirical power law derived from Landau theory and thus to obtain the value of the critical exponent. In contrast, the rigid-body approach did not fit the data as well. All parameterizations greatly reduce the number of required parameters. [source] The crystal structure of perdeuterated methanol hemiammoniate (CD3OD·0.5ND3) determined from neutron powder diffraction data at 4.2 and 180,KJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2010A. D. Fortes The crystal structure of perdeuterated methanol hemiammoniate, CD3OD·0.5ND3, has been solved from neutron powder diffraction data collected at 4.2 and 180,K. The structure is orthorhombic, space group Pn21a (Z = 4), with unit-cell dimensions a = 12.70615,(16), b = 8.84589,(9), c = 4.73876,(4),Å, V = 532.623,(8),Å3 [,calc = 1149.57,(2),kg,m,3] at 4.2,K, and a = 12.90413,(16), b = 8.96975,(8), c = 4.79198,(4),Å, V = 554.656,(7),Å3 [,calc = 1103.90,(1),kg,m,3] at 180,K. The crystal structure was determined by ab initio methods from the powder data; atomic coordinates and isotropic displacement parameters were subsequently refined by the Rietveld method to Rp, 2% at both temperatures. The crystal structure comprises a three-dimensionally hydrogen-bonded network in which the ND3 molecules are tetrahedrally coordinated by the hydroxy moieties of the methanol molecule. This connectivity leads to the formation of zigzag chains of ammonia,hydroxy groups extending along the c axis, formed via N,D···O hydrogen bonds; these chains are cross-linked along the a axis through the hydroxy moiety of the second methanol molecule via N,D···O and O,D···O hydrogen bonds. This `bridging' hydroxy group in turn donates an O,D···N hydrogen bond to ammonia in adjacent chains stacked along the b axis. The methyl deuterons in methanol hemiammoniate, unlike those in methanol monoammoniate, do not participate in hydrogen bonding and reveal evidence of orientational disorder at 180,K. The relative volume change on warming from 4.2 to 180,K, ,V/V, is + 4.14%, which is comparable to, but more nearly isotropic (as determined from the relative change in axial lengths, e.g.,a/a) than, that observed in deuterated methanol monohydrate, and very similar to what is observed in methanol monoammoniate. [source] Transformations for monoclinic crystal symmetry in texture analysisJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2009Siegfried Matthies Monoclinic crystals can be described in two settings: in the first setting the C2 rotation axis is parallel to the z axis and in the second setting it is parallel to the y axis. Transformations of lattice parameters, Miller and zone indices, and atomic coordinates is straightforward; the situation is far more complex for texture analysis with orientation distributions and corresponding representations. This article gives explicit transformations that need to be applied, not only for texture analysis but also for calculations of physical properties of materials with preferred orientation. In texture research the relationship between the Cartesian crystal coordinate system and the unit cell must be unambiguously defined and a uniform convention is desirable. [source] Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomoleculeJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2004Masaki Kojima A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data. [source] Bridging the gap , structure determination of the red polymorph of tetrahexylsexithiophene by Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinementJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2002Marcus A. Neumann The crystal structure of the red polymorph of tetrahexylsexithiophene (THST) is solved from X-ray powder diffraction data by a direct-space Monte Carlo simulated-annealing approach. First-principles density functional theory (DFT) calculations are used to distinguish between three nearly identical solutions in the space groups C2/m, C2 and P and to improve the overall accuracy of the crystal structure. The correct space group is found to be C2/m. In all space groups, the thiophene backbone is planar and the hexyl side chains assume an all- trans conformation except for two terminal methyl residues, which adopt a gauche orientation. The ability of first-principles DFT calculations to provide atomic coordinates of single-crystal quality is demonstrated by lattice-energy minimization of the known crystal structure of the yellow polymorph of THST. The combination of Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinement presented in this paper is generally applicable. It provides a powerful alternative to standard approaches in cases where the information content of the powder diffraction pattern alone is insufficient to distinguish between different structure solutions. DFT calculations can also provide invaluable guidance in Rietveld refinement. [source] ORTHON: transformation from triclinic axes and atomic coordinates to orthonormal onesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-2 2000Young-Soo Park First page of article [source] Toward accurate relative energy predictions of the bioactive conformation of drugsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Keith T. Butler Abstract Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol,1 of a local minimum, with penalties above 2.0kcal mol,1 being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] WATGEN: An algorithm for modeling water networks at protein,protein interfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2007Huynh-Hoa Bui Abstract Water molecules at protein,protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein,protein or protein,peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein,peptide interfaces (X-ray resolutions , 2.0 Å), using different criteria for water placement. The energies of the predicted water networks were evaluated in AMBER8 and used in the choice of parameters for WATGEN. The 126 interfaces include 1264 experimentally determined bridging water sites, and the WATGEN algorithm predicts 72 and 88% of these sites within 1.5 and 2.0 Å, respectively. The predicted number of water molecules at each interface was much higher than the number of water molecules identified experimentally. Therefore, random placement of the same number of water molecules as that predicted at each interface was performed as a control, and resulted in only 22 and 40% of water sites placed within 1.5 and 2.0 Å of experimental sites, respectively. Based on these data, we conclude that WATGEN can accurately predict the location of water molecules at a protein,peptide interface, and this may be of value for understanding the energetics and specificity of biomolecular association. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Calculation of the vibration frequencies of ,-quartz: The effect of Hamiltonian and basis setJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2004C. M. Zicovich-Wilson Abstract The central-zone vibrational spectrum of ,-quartz (SiO2) is calculated by building the Hessian matrix numerically from the analytical gradients of the energy with respect to the atomic coordinates. The nonanalytical part is obtained with a finite field supercell approach for the high-frequency dielectric constant and a Wannier function scheme for the evaluation of Born charges. The results obtained with four different Hamiltonians, namely Hartree,Fock, DFT in its local (LDA) and nonlocal gradient corrected (PBE) approximation, and hybrid B3LYP, are discussed, showing that B3LYP performs far better than LDA and PBE, which in turn provide better results than HF, as the mean absolute difference from experimental frequencies is 6, 18, 21, and 44 cm,1, respectively, when a split valence basis set containing two sets of polarization functions is used. For the LDA results, comparison is possible with previous calculations based on the Density Functional Perturbation Theory and usage of a plane-wave basis set. The effects associated with the use of basis sets of increasing size are also investigated. It turns out that a split valence plus a single set of d polarization functions provides frequencies that differ from the ones obtained with a double set of d functions and a set of f functions on all atoms by on average less than 5 cm,1. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1873,1881, 2004 [source] High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrityJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2003Robert F. Fischetti Wide-angle X-ray scattering patterns from proteins in solution contain information relevant to the determination of protein fold. At relevant scattering angles, however, these data are weak, and the degree to which they might be used to categorize the fold of a protein is unknown. Preliminary work has been performed at the BioCAT insertion-device beamline at the Advanced Photon Source which demonstrates that one can collect X-ray scattering data from proteins in solution to spacings of at least 2.2,Å (q = 2.8,Å,1). These data are sensitive to protein conformational states, and are in good agreement with the scattering predicted by the program CRYSOL using the known three-dimensional atomic coordinates of the protein. An important issue in the exploitation of this technique as a tool for structural genomics is the extent to which the high intensity of X-rays available at third-generation synchrotron sources chemically or structurally damage proteins. Various data-collection protocols have been investigated demonstrating conditions under which structural degradation of even sensitive proteins can be minimized, making this technique a viable tool for protein fold categorization, the study of protein folding, unfolding, protein,ligand interactions and domain movement. [source] Diffusion-equation method for crystallographic figure of meritsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2010Anders J. Markvardsen Global optimization methods play a significant role in crystallography, particularly in structure solution from powder diffraction data. This paper presents the mathematical foundations for a diffusion-equation-based optimization method. The diffusion equation is best known for describing how heat propagates in matter. However, it has also attracted considerable attention as the basis for global optimization of a multimodal function [Piela et al. (1989). J. Phys. Chem.93, 3339,3346]. The method relies heavily on available analytical solutions for the diffusion equation. Here it is shown that such solutions can be obtained for two important crystallographic figure-of-merit (FOM) functions that fully account for space-group symmetry and allow the diffusion-equation solution to vary depending on whether atomic coordinates are fixed or not. The resulting expression is computationally efficient, taking the same order of floating-point operations to evaluate as the starting FOM function measured in terms of the number of atoms in the asymmetric unit. This opens the possibility of implementing diffusion-equation methods for crystallographic global optimization algorithms such as structure determination from powder diffraction data. [source] A new approach to calculating powder diffraction patterns based on the Debye scattering equationACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010Noel William Thomas A new method is defined for the calculation of X-ray and neutron powder diffraction patterns from the Debye scattering equation (DSE). Pairwise atomic interactions are split into two contributions, the first from lattice-pair vectors and the second from cell-pair vectors. Since the frequencies of lattice-pair vectors can be directly related to crystallite size, application of the DSE is thereby extended to crystallites of lengths up to ~200,nm. The input data correspond to unit-cell parameters, atomic coordinates and displacement factors. The calculated diffraction patterns are characterized by full backgrounds as well as complete reflection profiles. Four illustrative systems are considered: sodium chloride (NaCl), ,-quartz, monoclinic lead zirconate titanate (PZT) and kaolinite. The effects of varying crystallite size on diffraction patterns are calculated for NaCl, quartz and kaolinite, and a method of modelling static structural disorder is defined for kaolinite. The idea of partial diffraction patterns is introduced and a treatment of atomic displacement parameters is included. Although the method uses pair distribution functions as an intermediate stage, it is anticipated that further progress in reducing computational times will be made by proceeding directly from crystal structure to diffraction pattern. [source] Structure determination without Fourier inversion.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009The parameter-space concept for solving crystal structures from reflection amplitudes (without employing or searching for their phases) is described on a theoretically oriented basis. Emphasis is placed on the principles of the method, on selecting one of three types of parameter spaces discussed in this paper, and in particular on the structure model employed (equal-atom point model, however usually reduced to one-dimensional projections) and on the system of `isosurfaces' representing experimental `geometrical structure amplitudes' in an orthonormal parameter space of as many dimensions as unknown atomic coordinates. The symmetry of the parameter space as well as of the imprinted isosurfaces and its effect on solution methods is discussed. For point atoms scattering with different phases or signs (as is possible in the case of X-ray resonant or of neutron scattering) it is demonstrated that the `landscape' of these isosurfaces remains invariant save certain shifts of origin known beforehand (under the condition that all atomic scattering amplitudes have been reduced to 1 thus meeting the requirement of the structure model above). Partly referring to earlier publications on the subject, measures are briefly described which permit circumventing an analytical solution of the system of structure-amplitude equations and lead to either a unique (unequivocal) approximate structure solution (offering rather high spatial resolution) or to all possible solutions permitted by the experimental data used (thus including also all potential `false minima'). A simple connection to Patterson vectors is given, also a first hint on data errors. References are given for practical details of various solution techniques already tested and for reconstruction of three-dimensional structures from their projections by `point tomography'. We would feel foolish if we tried to aim at any kind of `competition' to existing methods. Having mentioned `pros and cons' of our concept, some ideas about potential applications are nevertheless offered which are mainly based on its inherent resolution power though demanding rather few reflection data (use of optimal intensity contrast included) and possibly providing a result proven to be unique. [source] Dynameomics: Large-scale assessment of native protein flexibilityPROTEIN SCIENCE, Issue 12 2008Noah C. Benson Abstract Structure is only the first step in understanding the interactions and functions of proteins. In this paper, we explore the flexibility of proteins across a broad database of over 250 solvated protein molecular dynamics simulations in water for an aggregate simulation time of ,6 ,s. These simulations are from our Dynameomics project, and these proteins represent approximately 75% of all known protein structures. We employ principal component analysis of the atomic coordinates over time to determine the primary axis and magnitude of the flexibility of each atom in a simulation. This technique gives us both a database of flexibility for many protein fold families and a compact visual representation of a particular protein's native-state conformational space, neither of which are available using experimental methods alone. These tools allow us to better understand the nature of protein motion and to describe its relationship to other structural and dynamical characteristics. In addition to reporting general properties of protein flexibility and detailing many dynamic motifs, we characterize the relationship between protein native-state flexibility and early events in thermal unfolding and show that flexibility predicts how a protein will begin to unfold. We provide evidence that fold families have conserved flexibility patterns, and family members who deviate from the conserved patterns have very low sequence identity. Finally, we examine novel aspects of highly inflexible loops that are as important to structural integrity as conventional secondary structure. These loops, which are difficult if not impossible to locate without dynamic data, may constitute new structural motifs. [source] Quantitative description of the tilt of distorted octahedra in ABX3 structuresACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2007Rafael Tamazyan A description of the tilt of octahedra in ABX3 perovskite-related structures is proposed that can be used to extract the unique values for the tilt parameters ,, , and , of ABX3 structures with regular and distorted octahedra up to the point symmetry , from atomic coordinates and lattice parameters. The geometry of the BX6 octahedron is described by three B,X bond lengths (r1, r2, r3) and three X,B,X bond angles (,12, ,13 and ,23) or alternatively by a local strain tensor together with an average B,X bond length. Connections between the proposed method and Glazer's tilt system are discussed. The method is used to analyze structural transformations of I2/c, Pbnm and Immm structures. The proposed description allows the analysis of group,subgroup relations for the ABX3 structures with distorted octahedra, in terms of octahedral deformations and tilting. The method might also be of interest in the study of the phase transitions in the family of ABX3 structures. [source] Systematic prediction of new ferroelectrics in space groups P31 and P32ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2003S. C. Abrahams Release 2002/2 of the Inorganic Crystal Structure Database (FIZ Karlsruhe, Germany, and Institute Laue,Langevin, Grenoble, France) contains 62 entries in space group P31 and ten entries in space group P32 for 49 different materials including eight families with two or more isostructural members. The structural criteria for ferroelectricity are satisfied for 16 new structure types at a confidence level that depends on the reliability of each determination. LaBGeO5, a mineral with stillwellite structure, was previously reported as ferroelectric and forms an additional family with seven other members or related structures that satisfy the criteria. Ten structures reported in space group P31 or P32 are dubious or incorrect, with atomic coordinates that satisfy supergroup symmetry. One material is probably pyroelectric but is unlikely to become ferroelectric, and three others are either incompletely solved or incompletely refined. Among the predicted new ferroelectrics are Cu2BaGeS4, Fe3(Fe,Si)O4(OH)5, Se4S5, K2HCr2AsO10, IV-RbNO3, Rb2Sc(NO3)5, Na3ReO5, Nd14(GeO4)2(BO3)6O8, CsHgCl3, Ba2Cu2AlF11, KYF4, SrS2O6·4H2O, Cu3PbTeO6(OH)2, ReH(CO)4, Ni2(NH3)9Mo(CN)8·2H2O and the 6T polytype of Ca1.89Ta1.80Sm0.16Ti0.10O7, in addition to ,-LaBSiO5, PbBAsO5 and BaBAsO5 in the stillwellite family. [source] The assignment and validation of metal oxidation states in the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000Gregory P. Shields A methodology has been developed for the semi-automatic assignment and checking of formal oxidation states for metal atoms in the majority of metallo-organic complexes stored in the Cambridge Structural Database (CSD). The method uses both chemical connectivity and bond-length data, via ligand donor group templates and bond-valence sums, respectively. In order to use bond-length data, the CSD program QUEST has been modified to allow the coordination sphere of metal atoms to be recalculated using user-defined criteria at search time. The new methodology has been used successfully to validate the +1, +2 and +3 oxidation states in 743 four-coordinate copper complexes in the CSD for which atomic coordinates are available in ca 99% of structures using one or other method, and both succeed for >86% of structures. [source] Copper(II) chloride and bromide complexes with 2-methyl-2H -tetrazol-5-amine: an X-ray powder diffraction studyACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Ludmila S. Ivashkevich The complex catena -poly[[dibromidocopper(II)]-bis(,-2-methyl-2H -tetrazol-5-amine)-,2N4:N5;,2N5:N4], [CuBr2(C2H5N5)2]n, (I), and the isotypic chloride complex catena -poly[[dichloridocopper(II)]-bis(,-2-methyl-2H -tetrazol-5-amine)-,2N4:N5;,2N5:N4], [CuCl2(C2H5N5)2]n, (II), were investigated by X-ray powder diffraction at room temperature. The crystal structure of (I) was solved by direct methods, while the Rietveld refinement of (II) started from the atomic coordinates of (I). In both structures, the Cu atoms lie on inversion centres, adopting a distorted octahedral coordination of two halogen atoms, two tetrazole N atoms and two 5-amine group N atoms. Rather long Cu,Namine bonds allow consideration of the amine group as semi-coordinated. The compounds are one-dimensional coordination polymers, formed as a result of 2-methyl-2H -tetrazol-5-amine ligands bridging via a tetrazole N atom and the amine N atom. In the polymeric chains, adjacent Cu atoms are connected by two such bridges. [source] 4-Hydroxy-2-vinyl-2,3,4,5-tetrahydro-1-benzazepine and its 7-fluoro and 7-chloro analogues are isomorphous but not strictly isostructuralACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Lina M. Acosta 4-Hydroxy-2-vinyl-2,3,4,5-tetrahydro-1-benzazepine, C12H15NO, (I), and its 7-fluoro and 7-chloro analogues, namely 7-fluoro-4-hydroxy-2-vinyl-2,3,4,5-tetrahydro-1-benzazepine, C12H14FNO, (II), and 7-chloro-4-hydroxy-2-vinyl-2,3,4,5-tetrahydro-1-benzazepine, C12H14ClNO, (III), are isomorphous, but with variations in the unit-cell dimensions which preclude in compound (III) one of the weaker intermolecular interactions found in compounds (I) and (II). Thus the compounds are not strictly isostructural in terms of the structurally significant intermolecular interactions, although the corresponding atomic coordinates are very similar. The azepine rings adopt chair conformations. The molecules are linked by a combination of N,H...O and O,H...N hydrogen bonds into chains of edge-fused R33(10) rings, which in compounds (I) and (II) are further linked into sheets by a single C,H...,(arene) hydrogen bond. The significance of this study lies in its observation of isomorphism in compounds (I),(III), and its observation of a sufficient variation in one of the cell dimensions effectively to alter the range of significant hydrogen bonds present in the crystal structures. [source] Sr, Ba and Cd arsenates with the apatite-type structureACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2008Tamara ?ordevi X-ray diffraction analysis of single crystals of three new arsenates adopting apatite-type structures yielded formula Sr5(AsO4)3F for strontium arsenate fluoride, (I), (Sr1.66Ba0.34)(Ba2.61Sr0.39)(AsO4)3Cl for strontium barium arsenate chloride, (II), and Cd5(AsO4)3Cl0.58(OH)0.42 for cadmium arsenate hydroxide chloride, (III). All three structures are built up of isolated slightly distorted AsO4 tetrahedra that are bridged by Sr2+ in (I), by Sr2+/Ba2+ in (II) and by Cd2+ in (III). Compounds (I) and (II) represent typical fluorapatites and chlorapatites, respectively, with F, at the 2a (0, 0, ) site and Cl, at the 2b (0, 0, 0) site of P63/m. In contrast, in (III), due to the requirement that the smaller Cd2+ cation is positioned closer to the channel Cl, anion (partially substituted by OH,), the anion occupies the unusual 2a (0, 0, ) site. Therefore, Cl, is similar to F, in (I), coordinated by three A2 cations, unlike the octahedrally coordinated Cl, in (II) and other ordinary chlorapatites. Furthermore, in (III), using FT,IR studies, we have inferred the existence of H+ outside the channel in oxyhydroxyapatites and provided possible atomic coordinates for a H atom in HAsO42,, leading to a proposed formulation of the compound as Cd5(AsO4)3,x(HAsO4)xCl0.58(OH)0.42,x,(y/2)Ox+(y/2),y/2. [source] K2[HCr2AsO10]: redetermination of phase II and the predicted structure of phase IACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2004T. J. R. Weakley Our prediction that phase II of dipotassium hydrogen chromatoarsenate, K2[HCr2AsO10], is ferroelectric, based on the analysis of the atomic coordinates by Averbuch-Pouchot, Durif & Guitel [Acta Cryst. (1978), B34, 3725,3727], led to an independent redetermination of the structure using two separate crystals. The resulting improved accuracy allows the inference that the H atom is located in the hydrogen bonds of length 2.555,(5),Å which form between the terminal O atoms of shared AsO3OH tetrahedra in adjacent HCr2AsO102, ions. The largest atomic displacement of 0.586,Å between phase II and the predicted paraelectric phase I is by these two O atoms. The H atoms form helices of radius ,0.60,Å about the 31 or 32 axes. Normal probability analysis reveals systematic error in seven or more of the earlier atomic coordinates. [source] A new polymorph of cis,transoid,cis -dicyclohexano-18-crown-6.ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2003Erratum In the Comment of the paper by Kravtsov et al. [Acta Cryst. (2002), C58, o683o684], there in an error in a cited Cambridge Structural Database (Allen, 2002) refcode. The correct text is `Only recently, the atomic coordinates for the known monoclinic polymorph of the cis,transoid,cis isomer became available from a private communication (Nazarenko, 2002; CCDC refcode DCHXCS01).' The updated reference is given below. [source] A smooth and differentiable bulk-solvent model for macromolecular diffractionACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010T. D. Fenn Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute,solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, Rfree and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6,Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography. [source] Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57,GPaACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Isabella Ascone The 2,Å resolution crystal structure of bovine erythrocyte Cu,Zn superoxide dismutase (CuZnSOD) has been determined by X-ray diffraction at high pressure (0.57,GPa) and room temperature. At 0.57,GPa the secondary, tertiary and quaternary structures are similar to other previously determined bovine erythrocyte CuZnSOD structures. Nevertheless, pressure has a localized impact on the atomic coordinates of C, atoms and on side chains. The compression of the crystal and of the protein backbone is anisotropic. This anisotropy is discussed, taking into account intermolecular contacts and protein conformation. Pressure perturbation highlights the more flexible zones in the protein such as the electrostatic loop. At 0.57,GPa, a global shift of the dimetallic sites in both subunits and changes in the oxidation state of Cu were observed. The flexibility of the electrostatic loop may be useful for the interaction of different metal carriers in the copper-uptake process, whereas the flexibility of the metal sites involved in the activity of the protein could contribute to explaining the ubiquitous character of CuZnSODs, which are found in organisms living in very different conditions, including the deep-sea environment. This work illustrates the potential of combining X-ray crystallography with high pressure to promote and stabilize higher energy conformational substates. [source] Averaged kick maps: less noise, more signal,and probably less biasACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Jure Pra, nikar Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, they are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (,A) weighted. Analysis shows that they are comparable and correspond better to the final model than ,A and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation. [source] Confidence intervals for fitting of atomic models into low-resolution densitiesACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Niels Volkmann The fitting of high-resolution structures into low-resolution densities obtained from techniques such as electron microscopy or small-angle X-ray scattering can yield powerful new insights. While several algorithms for achieving optimal fits have recently been developed, relatively little effort has been devoted to developing objective measures for judging the quality of the resulting fits, in particular with regard to the danger of overfitting. Here, a general method is presented for obtaining confidence intervals for atomic coordinates resulting from fitting of atomic resolution domain structures into low-resolution densities using well established statistical tools. It is demonstrated that the resulting confidence intervals are sufficiently accurate to allow meaningful statistical tests and to provide tools for detecting potential overfitting. [source] The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-1 2004E. B. Krissinel The new CCP4 Coordinate Library is a development aiming to provide a common layer of coordinate-related functionality to the existing applications in the CCP4 suite, as well as a variety of tools that can simplify the design of new applications where they relate to atomic coordinates. The Library comprises a wide spectrum of useful functions, ranging from parsing coordinate formats and elementary editing operations on the coordinate hierarchy of biomolecules, to high-level functionality such as calculation of secondary structure, interatomic bonds, atomic contacts, symmetry transformations, structure superposition and many others. Most of the functions are available in a C++ object interface; however, a Fortran interface is provided for compatibility with older CCP4 applications. The paper describes the general principles of the Library design and the most important functionality. The Library, together with documentation, is available under the LGPL license from the CCP4 suite version 5.0 and higher. [source] Crystallization and preliminary X-ray analysis of Der f 2, a potent allergen derived from the house dust mite (Dermatophagoides farinae)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2003Dana Roeber Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophagoides sp.) are ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis and asthma associated with allergic reactions to these arthropods are frequently caused by relatively small (125,129 amino acids) mite proteins of unknown biological function. Der,f,2, a major allergen from the mite D.,farinae, has been recombinantly expressed, characterized and crystallized. The crystals belong to the tetragonal space group I4122, with unit-cell parameters a = b = 95.2, c = 103.3,Å. An essentially complete (97.2%) data set has been collected to 2.4,Å at a synchrotron source. Attempts to solve the crystal structure of Der,f,2 by molecular replacement using the NMR coordinates for either Der,f,2 or Der,p,2 (the homologous protein from D.,pteronyssinus) failed, but preliminary searches using the crystalline Der p 2 atomic coordinates appear to be promising. [source] | ||||||||||