Unit-cell Parameters (unit-cell + parameter)

Distribution by Scientific Domains

Kinds of Unit-cell Parameters

  • approximate unit-cell parameter
  • similar unit-cell parameter


  • Selected Abstracts


    Structure of strontium barium niobate SrxBa1,,,xNb2O6 (SBN) in the composition range 0.32 ,x, 0.82

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2006
    Sergey Podlozhenov
    The structure of strontium barium niobate crystals SrxBa1,,,xNb2O6 is comprehensively studied in the whole range of the tetragonal tungsten bronze phase (x = 0.32,0.82) using both powder and single-crystal X-ray diffraction measurements. Unit-cell parameters, density, site-occupancy factors and interionic distances show an explicit composition dependence which can be consistently explained using simple model calculations. The temperature dependence of the unit-cell parameters exhibits a remarkable anisotropy in a broad temperature region below the phase transition temperature. This proves that the electrostrictive contribution to the thermal expansion plays an important role in strontium barium niobate. [source]


    Generating isomorphous heavy-atom derivatives by a quick-soak method.

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2002
    Part II: phasing of new structures
    A quick-soak method has been applied to generate de novo heavy-atom phasing to solve two new protein structures, a type II transforming growth factor , receptor (TBRII) and a natural killer cell receptor,ligand complex, NKG2D,ULBP3. In the case of TBRII, a crystal derivatized for only 10,min in saturated HgCl2 provided adequate phasing for structure determination. Comparison between HgCl2 derivatives generated by 10,min soaking and by 12,h soaking revealed similar phasing statistics. The shorter soak, however, resulted in a derivative more isomorphous to the native than the longer soak as judged by changes in the unit-cell parameter a upon derivatization as well as by the quality of a combined SIRAS electron-density map. In the case of the NKG2D,ULBP3 structure, all overnight soaks in heavy-atom solutions resulted in crystal lattice disorder and only the quick soaks preserved diffraction. Despite fragile lattice packing, the quick-soaked K2PtCl4 derivative was isomorphous with the native crystal and the electron-density map calculated from combined SIR and MAD phases is better than that calculated from MAD phases alone. Combined with mass-spectrometry-assisted solution heavy-atom derivative screening and the use of synchrotron radiation, the quick-soak derivatization has the potential to transform the time-consuming conventional heavy-atom search into a real-time `on-the-fly' derivatization process that will benefit high-throughput structural genomics. [source]


    Crystallization and preliminary X-ray analysis of the full-size cubic core of pig 2-oxoglutarate dehydrogenase complex

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2002
    Kaoru Suzuki
    The full-length (untruncated) dihydrolipoamide succinyltransferase from pig heart was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction patterns indicate that the crystal belongs to space group I432, with unit-cell parameter a = 189.9,. The crystal structure has been preliminarily solved at 7, resolution by the molecular-replacement method. The unit cell contains two cubic cores, in each of which 24 subunits of E2 are associated according to crystallographic 432 symmetry. At the corners of each cubic core, the catalytic domains of E2s form a trimer through tight interactions around the crystallographic threefold axes. In the electron-density maps, many small broad peaks are observed in regions expected to contain the remaining N-terminal domains (the E1/E3-binding domain and the lipoyl domain), suggesting flexibility of these domains relative to the core. The architecture of the cubic core is similar to that of the other truncated E2s. In the unit cell, however, the core,core contact occurs in a different direction from that found for the truncated proteins. [source]


    Crystallization and preliminary crystallographic studies of the C-terminal domain of outer membrane protein A from enterohaemorrhagic Escherichia coli

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010
    Jiang Gu
    Outer membrane protein A (OmpA) of enterohaemorrhagic Escherichia coli (EHEC) plays multiple roles in bacterial physiology and pathogenesis, such as mediation of bacterial conjunction, maintenance of cell shape, induction of adhesion of EHEC to host cells etc. Better understanding of the functions of OmpA will help in the control of EHEC infections. OmpA is composed of two domains: the N-terminal domain and the C-terminal domain. The N-terminal domain is a ,-barrel structure and embeds in the outer membrane of the bacterium. The structure and function of the C-terminal domain of OmpA (OmpAC) remain elusive. In this study, recombinant OmpAC from EHEC was purified and crystallized and a diffraction data set was collected to 2.7, resolution. The crystals belonged to space group I4132, with unit-cell parameter a = 158.99,. The Matthews coefficient and solvent content were calculated to be 2.55,3,Da,1 and 51.77%, respectively, for two molecules in the asymmetric unit. [source]


    Crystallization and preliminary X-ray diffraction analysis of the complex of a human anti-ephrin type-A receptor 2 antibody fragment and its cognate antigen

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010
    Vaheh Oganesyan
    The recombinant N-terminal domain of human ephrin type-A receptor 2 (rEphA2) has been crystallized in complex with the recombinantly produced Fab fragment of a fully human antibody (1C1; IgG1/,). These are the first reported crystals of an ephrin receptor bound to an antibody. The orthorhombic crystals belonged to space group C2221 (the 00l reflections obey the l = 2n rule), with unit-cell parameters a = 78.93, b = 120.79, c = 286.20,. The diffraction of the crystals extended to 2.0, resolution. However, only data to 2.55, resolution were considered to be useful owing to spot overlap caused by the long unit-cell parameter. The asymmetric unit is most likely to contain two 1C1 Fab,rEphA2 complexes. This corresponds to a crystal volume per protein weight (VM) of 2.4,3,Da,1 and a solvent content of 49.5%. The three-dimensional structure of this complex will shed light on the molecular basis of 1C1 specificity. This will also contribute to a better understanding of the mechanism of action of this antibody, the current evaluation of which as an antibody,drug conjugate in cancer therapy makes it a particularly interesting case study. [source]


    Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2009
    Kohei Homma
    The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298,K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an amino-terminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65,. In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8,. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P213 IL-3A crystals with unit-cell parameter a = 105.68, and hexagonal P63 Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45,, , = 120. Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase. [source]


    The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2006
    Vinod B. Agarkar
    The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2,M sodium citrate, 400,mM NaCl, 100,mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96, resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4232, with unit-cell parameter a = 130.49 (0.05) . The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved. [source]


    The purification, crystallization and preliminary diffraction of a glycerophosphodiesterase from Enterobacter aerogenes

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2006
    Colin J. Jackson
    The metallo-glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) has been cloned, expressed in Escherichia coli and purified. Initial screening of crystallization conditions for this enzyme resulted in the identification of needles from one condition in a sodium malonate grid screen. Removal of the metals from the enzyme and subsequent optimization of these conditions led to crystals that diffracted to 2.9, and belonged to space group P213, with unit-cell parameter a = 164.1,. Self-rotation function analysis and VM calculations indicated that the asymmetric unit contains two copies of the monomeric enzyme, corresponding to a solvent content of 79%. It is intended to determine the structure of this protein utilizing SAD phasing from transition metals or molecular replacement. [source]


    Purification, crystallization and preliminary X-ray analysis of Mycobacterium tuberculosis folylpolyglutamate synthase (MtbFPGS)

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2006
    P. G. Young
    The gene encoding Mycobacterium tuberculosis FPGS (MtbFPGS; Rv2447c) has been cloned and the protein (51,kDa) expressed in Escherichia coli. The purified protein was crystallized either by the batch method in the presence of adenosine diphosphate (ADP) and CoCl2 or by vapour diffusion in the presence of ADP, dihydrofolate and CaCl2. X-ray diffraction data to approximately 2.0 and 2.6, resolution were collected at the Stanford Synchrotron Radiation Laboratory (SSRL) for crystals grown under the respective conditions. Both crystals belong to the cubic space group P213, with a unit-cell parameter of 112.6 and 111.8,, respectively. Structure determination is proceeding. [source]


    A Series of Lithium Rare Earth Polyphosphates [LiLn(PO3)4] (Ln = La, Eu, Gd) and Their Structural, Optical, and Electronic Properties

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2007
    Jing Zhu
    Abstract The structural, optical, and electronic properties of a series of lithium rare earth polyphosphates [LiLn(PO3)4] [Ln = La (1), Eu (2), Gd (3)] have been investigated by means of single-crystal X-ray diffraction, elemental analyses, and spectroscopic measurements, as well as calculations of energy-band structures, density of states, and optical response functions by density functional methods. These LiLn(PO3)4 systems are monoclinic with space group C2/c and Z = 4. Their unit-cell parameters decrease as the ionic radius of Ln3+ decreases (La3+ > Eu3+ > Gd3+). Both (PO4)3, zig-zag chains and infinite chains formed by the alternate connection of LnO8 polyhedra and LiO4 tetrahedra run parallel to the b -axis in the structure. The energy-band structures, density of states, the chemical bonds, and optical properties have been investigated by density functional methods for some of the title compounds. ( Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]


    Crystallization of Highly Supercooled Silicate Melts

    ADVANCED ENGINEERING MATERIALS, Issue 12 2006
    M. Roskosz
    Crystallization of liquids in the system CaO-MgO-Al2O3 -SiO2 at one atmosphere has been studied at temperatures between the glass transition (Tg) and the solidus. To determine the textures, compositions and unit-cell parameters of the crystalline phases, the authors have characterized the experimental charges over a wide range of length scales by scanning and transmission electron microscopy, electron microprobe analyses, X-ray diffraction, and Raman spectroscopy. With increasing temperature, crystals tend to reach the equilibrium composition, but the relative importance of thermodynamic and kinetic factors is a single function of T - Tg, regardless of liquid composition. This feature is of considerable practical interest as it provides the possibility, not only to predict, but also to control the composition of the crystallizing phases. [source]


    In-house characterization of protein powder

    JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2010
    Christian Grundahl Hartmann
    X-ray powder diffraction patterns of lysozyme and insulin were recorded on a standard in-house powder diffractometer. The experimental powder diffraction patterns were compared with patterns calculated from Protein Data Bank coordinate data. Good agreement was obtained by including straightforward corrections for background, unit-cell parameters, disordered bulk solvent and geometric factors. In particular the solvent correction was found crucial for a good agreement. A revised Lorentz factor was derived, which gave a minor, but significant, improvement to the fit in the low-angle region. An attempt to include calculated H-atom positions did not improve the overall fit and was abandoned. The method devised was shown to be a quick and convenient tool for distinguishing precipitates and polymorphs of proteins. [source]


    Energetic materials: variable-temperature crystal structure of ,-NTO

    JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003
    Nadezhda B. Bolotina
    The crystal structure of the metastable , form of 5-nitro-2,4-dihydro-3H -1,2,4-triazol-3-one (,-NTO, monoclinic, P21/c) has been investigated at five temperatures in the range 100,298,K using single-crystal X-ray diffraction techniques. The second-rank thermal expansion tensor has been determined to describe thermal behavior of the crystal. The most significant thermal expansion is in a plane, which is almost perpendicular to the planes of all the NTO molecules. Perpendicular to the plane of maximal thermal expansion, a modest thermal contraction takes place. Both thermal expansion and contraction of the crystal lattice indicate anharmonicity of the atomic thermal motion. The experimental thermal variation of the unit-cell parameters is in qualitative agreement with that previously obtained from molecular dynamics calculations. Rigid-body analysis of the molecular thermal motion was performed using the libration and translation second-rank tensors. Although the translation part of the thermal motion is not strongly anisotropic, the largest displacements of the NTO molecules are oriented in the plane of maximal thermal expansion of the crystal and have significant anharmonic components. The libration motion is more anisotropic, and the largest libration as well as the largest translation principal axes are directed along the C5,N5 bond in each NTO molecule. [source]


    A new approach to calculating powder diffraction patterns based on the Debye scattering equation

    ACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010
    Noel 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]


    Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthrones

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010
    Martin U. Schmidt
    The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P21/c, Z = 2, the dichloro derivative in , Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes in P21/c, Z = 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom,atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom,atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph. [source]


    Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010
    Jacco Van De Streek
    This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095, (0.084, for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25, either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect. [source]


    Reversible phase transition of pyridinium-3-carboxylic acid perchlorate

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010
    Heng-Yun Ye
    Pyridinium-3-carboxylic acid perchlorate was synthesized and separated as crystals. Differential scanning calorimetry (DSC) measurements show that this compound undergoes a reversible phase transition at ,,135,K with a wide hysteresis of 15,K. Dielectric measurements confirm the transition at ,,127,K. Measurement of the unit-cell parameters versus temperature shows that the values of the c axis and , angle change abruptly and remarkably at 129,(2),K, indicating that the system undergoes a first-order transition at Tc = 129,K. The crystal structures determined at 103 and 298,K are all monoclinic in P21/c, showing that the phase transition is isosymmetric. The crystal contains one-dimensional hydrogen-bonded chains of the pyridinium-3-carboxylic acid cations, which are further linked to perchlorate anions by hydrogen bonds to form well separated infinite planar layers. The most distinct differences between the structures of the higher-temperature phase and the lower-temperature phase are the change of the distance between the adjacent pyridinium ring planes within the hydrogen-bonded chains and the relative displacement between the hydrogen-bonded layers. Structural analysis shows that the driving force of the transition is the reorientation of the pyridinium-3-carboxylic acid cations. The degree of order of the perchlorate anions may be a secondary order parameter. [source]


    Incommensurately modulated lanthanide coinage-metal diarsenides.

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009

    Rare-earth metal coinage-metal diarsenides LnTAs2 (Ln = Y, La, Ce,Lu; T = Cu, Ag, Au) are known to crystallize in structures closely related to the HfCuSi2 type, which comprises a stacking sequence of puckered TAs layers and planar square As nets, separated by the Ln atoms. CeAu1,,As2, with , = 0.015,(2), shows an incommensurate positional modulation of the arsenic atoms in the planar As nets. Based on X-ray diffraction data on a twinned crystal, a structure model in the monoclinic superspace group P121/m1(,0,)00 (No. 11.1) with basic unit-cell parameters of a = 5.804,(1), b = 5.814,(1), c = 10.179,(1), and , = 90.09,(8) is presented. The components of the modulation wavevector q = ,a* + 0b* + ,c* are , = 0.08,(1) and , = 0.39,(1). The structure comprises cis,trans chains and rectangles of As atoms and displays an intricate stacking sequence of the modulated arsenic nets. Rod groups and layer groups of the respective arrangements are identified and the arrangement of different motifs of the modulated As net is discussed. [source]


    Capabilities and limitations of a (3,+,d)-dimensional incommensurately modulated structure as a model for the derivation of an extended family of compounds: example of the scheelite-like structures

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2008
    Alla Arakcheeva
    The previously reported incommensurately modulated scheelite-like structure KNd(MoO4)2 has been exploited as a natural (3,+,1)-dimensional superspace model to generate the scheelite-like three-dimensional structure family. Although each member differs in its space-group symmetry, unit-cell parameters and compositions, in (3,+,1)-dimensional space, they share a common superspace group, a common number of building units in the basic unit cell occupying Wyckoff sites with specific coordinates (x, y, z) and specific basic unit-cell axial ratios (c/a, a/b, b/c) and angles. Variations of the modulation vector q, occupation functions and t0 are exploited for the derivation. Eight topologically and compositionally different known structures are compared with their models derived from the KNd(MoO4)2 structure in order to evaluate the capabilities and limitations of the incommensurately modulated structure to act as a superspace generating model. Applications of the KNd(MoO4)2 structure as a starting model for the refinement and prediction of some other modulated members of the family is also illustrated. The (3,+,1)-dimensional presentation of the scheelite-like structures reveals new structural relations, which remain hidden if only conventional three-dimensional structure descriptions are applied. [source]


    Structure of strontium barium niobate SrxBa1,,,xNb2O6 (SBN) in the composition range 0.32 ,x, 0.82

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2006
    Sergey Podlozhenov
    The structure of strontium barium niobate crystals SrxBa1,,,xNb2O6 is comprehensively studied in the whole range of the tetragonal tungsten bronze phase (x = 0.32,0.82) using both powder and single-crystal X-ray diffraction measurements. Unit-cell parameters, density, site-occupancy factors and interionic distances show an explicit composition dependence which can be consistently explained using simple model calculations. The temperature dependence of the unit-cell parameters exhibits a remarkable anisotropy in a broad temperature region below the phase transition temperature. This proves that the electrostrictive contribution to the thermal expansion plays an important role in strontium barium niobate. [source]


    New model for the hydroxyapatite,octacalcium phosphate interface

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2003
    M. E. Fernndez
    Some experimental results have indicated that hydroxyapatite (HA) and octacalcium phosphate (OCP) can form an epitaxic interface. Subsequently the OCP,HA interface has become of great biological interest in the context of mineralized tissue formation. In this work a new OCP,HA interface model based on Brown's proposed configuration [Brown (1962), Nature, 197, 1048,1050] and using the minimum interface free-energy optimization is presented. This new model is formed by half a unit cell of HA and one unit cell of OCP, as in Brown's model, but in our case [110] of HA is `glued' with [010] of OCP. Therefore, the relationship found was: [000]HA parallel to [001]OCP and [110]HA parallel to [010]OCP. Self-consistent field methods were used for the analysis of Brown's model and ours. It is shown that the atoms in our model have similar environments as in the HA and OCP unit cells and that, as a result of the differences between HA and OCP unit-cell parameters, this interface presents misfit-dislocation-like features. High-resolution transmission electron microscopy (HREM) simulated images for the new interface model have been included and, when they are compared with the experimental ones, the similarity is quite good. [source]


    Structure solution of the basic decagonal Al,Co,Ni phase by the atomic surfaces modelling method

    ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2002
    Antonio Cervellino
    The atomic surfaces modelling technique has been used to solve the structure of the basic Ni-rich Al,Co,Ni decagonal phase. Formula Al70.6Co6.7Ni22.7, space group , five-dimensional unit-cell parameters: d1 = d4 = 4.752,(3),, d2 = d3 = 3.360,(2),, d5 = 8.1710,(2),; ,12 = ,34 = 69.295, ,13 = ,24 = 45, ,14 = 41.410, ,23 = ,i5 = 90 (i = 1,4), V = 291.2,(7),5; Dx = 3.887,Mg,m,3. Refinement based on |F|; 2767 unique reflections (|F| > 0), 749 parameters, R = 0.17, wR = 0.06. Describing the structure of quasicrystals embedded in n -dimensional superspace in principle takes advantage of n -dimensional periodicity to select the minimal set of degrees of freedom for the structure. The method of modelling of the atomic surfaces yielded the first fully detailed structure solution of this phase. Comparison with numerous former, less accurate models confirms several features already derived, but adds a new essential insight of the structure and its complexity. The atoms fill the space forming recurrent structure motifs, which we will (generically) refer to as clusters. However, no unique cluster exists, although differences are small. Each cluster shows a high degree of structural disorder. This gives rise to a large configurational entropy, as much as expected in a phase which is stable at high temperature. On the other side, the cluster spatial arrangement is perfectly quasiperiodic. These considerations, corroborated by analysis of the structural relationship with neighbouring periodic phases, strongly suggest the existence of a non-local, long-range interaction term in the total energy which may be essential to the stability. [source]


    A new modification of thallium chromate related to the ,-K2SO4 family

    ACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2010
    Jan Fbry
    The title structure is a new modification of Tl2CrO4. There are four independent Tl+ cations and two [CrO4]2, anions in the structure. It is closely related to the already known modification, which belongs to the ,-K2SO4 family with two independent cations and one anion. In both modifications, the cations and anions are situated on crystallographic mirror planes. The volume of the asymmetric unit of the title structure is ,0.4% smaller than that of the known modification belonging to the ,-K2SO4 family. The other difference between the two modifications is seen in the environment of the cations. In the title structure, none of the Tl+ cations is underbonded, in contrast with the modification isostructural with ,-K2SO4. In the ,-K2SO4 family with simple cations, underbonding of one of the constituent cations is typical. The dependence of the unit-cell parameters on temperature does not indicate a phase transition in the interval 90,300,K. [source]


    Two regioisomers of condensed thioheterocyclic triazine synthesized from 6-phenyl-3-thioxo-2,3,4,5-tetrahydro-1,2,4-triazin-5-one

    ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009
    Akiko Hori
    In the crystal structure of 6-phenyl-3-thioxo-2,3,4,5-tetrahydro-1,2,4-triazin-5-one, C9H7N3OS, (I), the 1,2,4-triazine moieties are connected by face-to-face contacts through two kinds of double hydrogen bonds (N,H...O and N,H...S), which form planar ribbons along the a axis. The ribbons are crosslinked through C,H..., interactions between the phenyl rings. The molecular structures of two regioisomeric compounds, namely 6-phenyl-2,3-dihydro-7H -1,3-thiazolo[3,2- b][1,2,4]triazin-7-one, C11H9N3OS, (II), and 3-phenyl-6,7-dihydro-4H -1,3-thiazolo[2,3- c][1,2,4]triazin-4-one, C11H9N3OS, (III), which were prepared by the condensation reaction of (I) with 1,2-dibromoethane, have been characterized by X-ray crystallography and spectroscopic studies. The crystal structures of (II) and (III) both show two crystallographically independent molecules. While the two compounds are isomers, the unit-cell parameters and crystal packing are quite different and (II) has a chiral crystal structure. [source]


    A structural systematic study of four isomers of difluoro- N -(3-pyridyl)benzamide

    ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009
    Joyce McMahon
    The four isomers 2,4-, (I), 2,5-, (II), 3,4-, (III), and 3,5-difluoro- N -(3-pyridyl)benzamide, (IV), all with formula C12H8F2N2O, display molecular similarity, with interplanar angles between the C6/C5N rings ranging from 2.94,(11) in (IV) to 4.48,(18) in (I), although the amide group is twisted from either plane by 18.0,(2),27.3,(3). Compounds (I) and (II) are isostructural but are not isomorphous. Intermolecular N,H...O=C interactions form one-dimensional C(4) chains along [010]. The only other significant interaction is C,H...F. The pyridyl (py) N atom does not participate in hydrogen bonding; the closest H...Npy contact is 2.71, in (I) and 2.69, in (II). Packing of pairs of one-dimensional chains in a herring-bone fashion occurs via,-stacking interactions. Compounds (III) and (IV) are essentially isomorphous (their a and b unit-cell lengths differ by 9%, due mainly to 3,4-F2 and 3,5-F2 substitution patterns in the arene ring) and are quasi-isostructural. In (III), benzene rotational disorder is present, with the meta F atom occupying both 3- and 5-F positions with site occupancies of 0.809,(4) and 0.191,(4), respectively. The N,H...Npy intermolecular interactions dominate as C(5) chains in tandem with C,H...Npy interactions. C,H...O=C interactions form R22(8) rings about inversion centres, and there are ,,, stacks about inversion centres, all combining to form a three-dimensional network. By contrast, (IV) has no strong hydrogen bonds; the N,H...Npy interaction is 0.3, longer than in (III). The carbonyl O atom participates only in weak interactions and is surrounded in a square-pyramidal contact geometry with two intramolecular and three intermolecular C,H...O=C interactions. Compounds (III) and (IV) are interesting examples of two isomers with similar unit-cell parameters and gross packing but which display quite different intermolecular interactions at the primary level due to subtle packing differences at the atom/group/ring level arising from differences in the peripheral ring-substitution patterns. [source]


    Apparent shortening of the Csp3,Csp3 bond analysed via a variable-temperature X-ray diffraction study in racemic 1,1,-binaphthalene-2,2,-diyl diethyl bis(carbonate)

    ACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009
    Susanta K. Nayak
    Crystal structure determination at room temperature [292,(2),K] of racemic 1,1,-binaphthalene-2,2,-diyl diethyl bis(carbonate), C26H22O6, showed that one of the terminal carbon,carbon bond lengths is very short [Csp3,Csp3 = 1.327,(6),]. The reason for such a short bond length has been analysed by collecting data sets on the same crystal at 393, 150 and 90,K. The values of the corrected bond lengths clearly suggest that the shortening is mainly due to positional disorder at two sites, with minor perturbations arising as a result of thermal vibrations. The positional disorder has been resolved in the analysis of the 90,K data following the changes in the unit-cell parameters for the data sets at 150 and 90,K, which appear to be an artifact of a near centre of symmetry relationship between the two independent molecules in the space group P at these temperatures. Indeed, the unit cell at low temperature (150 and 90,K) is a supercell of the room-temperature unit cell. [source]


    Structure of d -tyrosyl-tRNATyr deacylase using home-source Cu,K, and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010
    Manickam Yogavel
    d -Tyrosyl-tRNATyr deacylase (DTD) is an editing enzyme that removes d -amino acids from mischarged tRNAs. The crystal structure of Plasmodium falciparum DTD (PfDTD) was determined using the iodide-SAD phasing method. Iodide-derivatized PfDTD crystals were obtained using the quick cryo-soaking procedure in which native crystals were soaked for a short period of 10,30,s in cryoprotectant solution containing 0.2,1,M NaI. Iodide-SAD data sets were collected to 3.3 and 2.74, resolution from PfDTD crystals that belonged to two different space groups, P43 and P1, using an in-house X-ray copper-anode source. This is the first report to detail structure solution using low iodide anomalous signal, modest resolution and redundancy and average solvent content for SAD phasing of 984 and 1312 amino acids in the triclinic P1 and tetragonal P43 space groups, respectively. A total of 85% and 56% of the residues were automatically built into the iodide-phased electron-density maps using PHENIX AutoBuild. The structure of HEPES-bound PfDTD was subsequently determined by molecular replacement and refined to 2.83, resolution. The crystals obtained from various batches of crystallization trials of PfDTD exhibited polymorphism in terms of belonging to different crystal forms and space groups. Even within a given crystal system the unit-cell parameters showed high non-isomorphism. These packing variations were exploited in order to conduct a systematic study of conformational changes in PfDTD. It is shown that the disposition of a ten-residue insertion loop affects packing within the PfDTD crystals and seems to determine the non-isomorphism in unit-cell parameters. By tracking the changes in PfDTD unit cells, it was possible to map conformational differences within PfDTD that may be of significance for enzyme activity. [source]


    Structure of grouper iridovirus purine nucleoside phosphorylase

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2010
    You-Na Kang
    Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides to the corresponding free bases and ribose 1-phosphate. The crystal structure of grouper iridovirus PNP (givPNP), corresponding to the first PNP gene to be found in a virus, was determined at 2.4, resolution. The crystals belonged to space group R3, with unit-cell parameters a = 193.0, c = 105.6,, and contained four protomers per asymmetric unit. The overall structure of givPNP shows high similarity to mammalian PNPs, having an ,/, structure with a nine-stranded mixed ,-barrel flanked by a total of nine ,-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively. The geometrical arrangement and hydrogen-bonding patterns of the phosphate-binding site are similar to those found in the human and bovine PNP structures. The enzymatic activity assay of givPNP on various substrates revealed that givPNP can only accept 6-oxopurine nucleosides as substrates, which is also suggested by its amino-acid composition and active-site architecture. All these results suggest that givPNP is a homologue of mammalian PNPs in terms of amino-acid sequence, molecular mass, substrate specificity and overall structure, as well as in the composition of the active site. [source]


    Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCR, fragments

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2010
    Walter M. Kim
    HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling , subunit of the T-cell receptor (TCR,). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCR, fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCR, polypeptide (Leu51,Asp93) was determined to 3.7, resolution (Rwork = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCR, polypeptide (Ala63,Arg80) was determined to 2.05, resolution (Rwork = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P212121. The reduction in crystal space-group symmetry induced by the truncated TCR, polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, ,l) and a and b unit-cell parameters that were nearly identical predisposed the P212121 crystal form to pseudo-merohedral twinning. [source]


    Two crystal modifications of (Pro-Pro-Gly)4 -Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010
    Kenji Okuyama
    Two crystal modifications of a collagen model peptide, (Pro-Pro-Gly)4 -Hyp-Hyp-Gly-(Pro-Pro-Gly)4 [where Hyp is (4R,2S)- l -hydroxyproline], showed very similar unit-cell parameters and belonged to the same space group P21. Both crystals exhibited pseudo-merohedral twinning. The main difference was in their molecular-packing arrangements. One modification showed pseudo-hexagonal packing, while the other showed pseudo-tetragonal packing. Despite their different packing arrangements, no significant differences were observed in the hydration states of these modifications. The peptide in the pseudo-tetragonal crystal showed a cyclic fluctuation of helical twists with a period of 20,, while that in the pseudo-hexagonal crystal did not. In these modifications, the puckering conformations of four of the 12 Hyp residues at the X position of the Hyp(X)-Hyp(Y)-Gly sequence were in the opposite conformations to the previous hypothesis that Hyp(X) residues involved in Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs prefer up-puckering and down-puckering conformations, respectively. Detailed investigation of the molecular interactions between Hyp(X) and adjacent molecules revealed that these opposite conformations appeared because the puckering conformation, which follows the hypothesis, is subject to steric hindrance from the adjacent molecule. [source]