Home About us Contact
|
Home About us Contact | ||
|
|
||
Refined Structure (refined + structure)
Selected AbstractsDetermination of zinc incorporation in the Zn-substituted gallophosphate ZnULM-5 by multiple wavelength anomalous dispersion techniquesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010M. Helliwell The location of isomorphously substituted zinc over eight crystallographically different gallium sites has been determined in a single-crystal study of the gallophosphate ZnULM-5, GaZn(PO4)14(HPO4)2(OH)2F7, [H3N{CH2}6NH3]4, 6H2O, in an 11 wavelength experiment, using data from Station 9.8, SRS Daresbury. The measurement of datasets around the K edges of both Ga and Zn, as well as two reference datasets away from each absorption edge, was utilized to selectively exploit dispersive differences of each metal atom type in turn, which allowed the major sites of Zn incorporation to be identified as the metal 1 and 3 sites, M1 and M3. The preferential substitution of Zn at these sites probably arises because they are located in double four-ring (D4R) building units which can relax to accommodate the incorporation of hetero atoms. As the crystal is non-centrosymmetric, with space group P21212, it was also possible to use anomalous differences to corroborate the results obtained from the dispersive differences. These results were obtained firstly from difference Fourier maps, calculated using a phase set from the refined structure from data measured at the Zr K edge. Also, refined dispersive and anomalous occupancies, on an absolute scale, could be obtained using the program MLPHARE, allowing estimates for the Zn incorporation of approximately 22 and 18 at. % at the M1 and M3 sites to be obtained. In addition, f, and f,, values for Ga and Zn at each wavelength could be estimated both from MLPHARE results, and by refinement in JANA2006. The fully quantitative determinations of the dispersive and anomalous coefficients for Ga and Zn at each wavelength, as well as metal atom occupancies over the eight metal atom sites made use of the CCP4's MLPHARE program as well as SHELXL and JANA2006. The results by these methods agree closely, and JANA2006 allowed the ready determination of standard uncertainties on the occupancy parameters, which were for M1 and M3, 20.6,(3) and 17.2,(3),at %, respectively. [source] Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Edward E. Ávila The molecular and crystalline structure of ethyl 1,,2,,3,,4,,4a,,5,,6,,7,-octahydrodispiro[cyclohexane-1,2,-quinazoline-4,,1,,-cyclohexane]-8,-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst.39, 910,915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem.38, 1223,1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N,H...S and C,H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions. [source] Crystal structures and cation ordering in Cs2MgSi5O12, Rb2MgSi5O12 and Cs2ZnSi5O12 leucitesACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2009A. M. T. Bell The crystal structures of the leucite analogues Cs2MgSi5O12, Cs2ZnSi5O12 and Rb2MgSi5O12 have been determined by synchrotron X-ray powder diffraction using Rietveld refinement in conjunction with 29Si MAS NMR spectroscopy. These leucites are framework structures with distinct tetrahedral sites (T sites) occupied by Si and a divalent cation (either Mg or Zn in these samples); there is also a monovalent extra-framework cation (either Cs or Rb in these samples). The refined crystal structures were based on the Pbca leucite structure of Cs2CdSi5O12, thus a framework with five ordered Si T sites and one ordered Cd T site was used as the starting model for refinement. 29Si MAS NMR shows five distinct Si T sites for Cs2MgSi5O12 and Rb2MgSi5O12, but six Si T sites for Cs2ZnSi5O12. The refined structures for Cs2MgSi5O12 and Rb2MgSi5O12 were determined with complete T -site ordering, but the refined structure for Cs2ZnSi5O12 was determined with partial disorder of Mg and Si over two of the T sites. [source] Type II dehydroquinase: molecular replacement with many copiesACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2008Kirsty Anne Stewart Type II dehydroquinase is a small (150-amino-acid) protein which in solution packs together to form a dodecamer with 23 cubic symmetry. In crystals of this protein the symmetry of the biological unit can be coincident with the crystallographic symmetry, giving rise to cubic crystal forms with a single monomer in the asymmetric unit. In crystals where this is not the case, multiple copies of the monomer are present, giving rise to significant and often confusing noncrystallographic symmetry in low-symmetry crystal systems. These different crystal forms pose a variety of challenges for solution by molecular replacement. Three examples of structure solutions, including a highly unusual triclinic crystal form with 16 dodecamers (192 monomers) in the unit cell, are described. Four commonly used molecular-replacement packages are assessed against two of these examples, one of high symmetry and the other of low symmetry; this study highlights how program performance can vary significantly depending on the given problem. In addition, the final refined structure of the 16-dodecamer triclinic crystal form is analysed and shown not to be a superlattice structure, but rather an F -centred cubic crystal with frustrated crystallographic symmetry. [source] Real-space protein-model completion: an inverse-kinematics approachACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2005Henry Van Den Bedem Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map. In favorable circumstances, various software systems are capable of building over 90% of the final model. However, completeness falls off rapidly with the resolution of the diffraction data. Manual completion of these partial models is usually feasible, but is time-consuming and prone to subjective interpretation. Except for the N- and C-termini of the chain, the end points of each missing fragment are known from the initial model. Hence, fitting fragments reduces to an inverse-kinematics problem. A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points. The first stage samples a large number of closing conformations, guided by the electron density. These candidates are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of conformation space to preserve rigid geometry and closure. Experimental results show that fitted fragments are in excellent agreement with the final refined structure for lengths of up to 12,15 residues in areas of weak or ambiguous electron density, even at medium to low resolution. [source] Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87,AACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Jan Massant Using synchrotron radiation, X-ray data have been collected from Pyrococcus furiosus ornithine carbamoyltransferase (Pfu OTCase) to a maximal resolution of 1.87,Å, allowing the refinement of a previous structure at 2.7,Å [Villeret et al. (1998), Proc. Natl Acad. Sci. USA, 95, 2801,2806]. Thanks to the high resolution of this refined structure, two sulfate ions and 191 water molecules could be localized directly from the electron-density maps. The identification of these molecules allowed a more rigorous description of the active site and the identification of residues involved in binding carbamoyl phosphate. The improved quality of the model resulted in a better definition of several loops and the various interfaces. The dodecameric protein is composed of four catalytic trimers disposed in a tetrahedral manner. The extreme thermal stability of Pfu OTCase is mainly the result of the strengthening of the intersubunit interactions in a trimer and oligomerization of the trimers into a dodecamer. Interfaces between monomers in a catalytic trimer are characterized by an increase in ion-pair networks compared with mesophilic OTCases. However, the interfaces between catalytic trimers in the dodecameric oligomer are mainly hydrophobic and also involve aromatic,aromatic and cation,, interactions. [source] High-pressure single-crystal X-ray diffraction facilities on station 9.8 at the SRS Daresbury Laboratory , hydrogen location in the high-pressure structure of ethanolJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2001David R. Allan A new high-pressure single-crystal diffraction facility has been constructed on station 9.8 at the Synchrotron Radiation Source, Daresbury Laboratory, for a range of studies on a variety of systems of relevance to physics, chemistry and materials science that would otherwise prove intractable with conventional laboratory-based methods. The station has been equipped with a modified Enraf,Nonius CAD4 four-circle diffractometer for high-pressure studies which can be conveniently, and rapidly, interchanged with the Bruker SMART CCD area-detector system when more routine ambient-pressure diffraction work is to be undertaken. This rapid change-over has been achieved by permanently mounting the CAD4 on its own jacking table, formerly used for the station's white-beam diffraction mode, which allows the alignment of the SMART diffractometer to remain undisturbed when the CAD4 is in use. Early results on the test low-melting-point compound ethanol (CH3CH2OH) reveal that excellent refined structures can be obtained, including the location and refinement of the H atoms, demonstrating that one of the original, and major, objectives of the station has been accomplished. [source] A dipicolinate lanthanide complex for solving protein structures using anomalous diffractionACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Guillaume Pompidor Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic elastase and xylanase from Trichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinic C2 crystal form that diffracted to high resolution. [source] Heavy-atom derivatives in lipidic cubic phases: results on hen egg-white lysozyme tetragonal derivative crystals with Gd-HPDO3A complexACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2004Éric Girard Gd-HPDO3A, a neutral gadolinium complex, is a good candidate for obtaining heavy-atom-derivative crystals by the lipidic cubic phase crystallization method known to be effective for membrane proteins. Gadolinium-derivative crystals of hen egg-white lysozyme were obtained by co-crystallizing the protein with 100,mM Gd-HPDO3A in a monoolein cubic phase. Diffraction data were collected to a resolution of 1.7 Å using Cu,K, radiation from a rotating-anode generator. Two binding sites of the gadolinium complex were located from the strong gadolinium anomalous signal. The Gd-atom positions and their refined occupancies were found to be identical to those found in derivative crystals of hen egg-white lysozyme obtained by co-crystallizing the protein with 100,mM Gd-HPDO3A using the hanging-drop technique. Moreover, the refined structures are isomorphous. The lipidic cubic phase is not disturbed by the high concentration of Gd-HPDO3A. This experiment demonstrates that a gadolinium complex, Gd-HPDO3A, can be used to obtain derivative crystals by the lipidic cubic phase crystallization method. Further studies with membrane proteins that are known to crystallize in lipidic cubic phases will be undertaken with Gd-HPDO3A and other Gd complexes to test whether derivative crystals with high Gd-site occupancies can be obtained. [source] High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5,AMPACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001Pascal Retailleau Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS,adenylate product (TAM) complex to a resolution limit of 1.7,Å. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS combinations with native data. Hendrickson,Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9,Å structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25,Å and from the native model by 0.38,Å, but all have r.m.s. deviations of ,1.0,Å from the 2.9,Å model. Difference Fourier calculations between amplitudes from the 300,K experiment and the new amplitudes at 100,K using 1.7,Å model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria. [source] | ||||||||||