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Structural Refinement (structural + refinement)
Selected AbstractsCrystal Growth and Structural Refinement of NaMn7O12.CHEMINFORM, Issue 1 2006E. Gilioli Abstract For Abstract see ChemInform Abstract in Full Text. [source] P,T Phase Diagram and Single Crystal Structural Refinement of NaMn7O12.CHEMINFORM, Issue 37 2005Edmondo Gilioli Abstract For Abstract see ChemInform Abstract in Full Text. [source] Structural Refinement of the High-Pressure Phase of Aluminum Trihydroxide: In situ High-Pressure Angle Dispersive Synchrotron X-Ray Diffraction and Theoretical Studies.CHEMINFORM, Issue 33 2005Haozhe Liu Abstract For Abstract see ChemInform Abstract in Full Text. [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] Dose dependence of radiation damage for protein crystals studied at various X-ray energiesJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2007Nobutaka Shimizu Radiation damage to protein crystals is the most serious problem in obtaining accurate structures from protein crystallography. In order to examine the photon energy dependence of radiation damage, 12 to 15 data sets from each of nine tetragonal lysozyme crystals were collected at nine different X-ray energies (6.5, 7.1, 8.3, 9.9, 12.4, 16.5, 20.0, 24.8 and 33.0,keV) using beamline BL41XU at SPring-8. All results were compared on the basis of absorbed dose, expressed in Gray (Gy). Crystallographic statistics, such as the values of lattice constants, Rmerge and I/,(I), for each data set degraded at all nine energies as the exposure time for each crystal increased. In all data sets, radiation damage was observed after the absorbed dose exceeded 106,Gy. However, from the point of view of crystallographic statistics normalized to the absorbed dose, no clear dependence on photon energy was observed in these results. Structural refinement showed that the average B -factor for the last data set was larger than that for the first data set at all energies tested. However, no energy dependence of radiation damage on B -factor was found. Furthermore, disruption of disulfide bonds due to radiation damage was observed in electron density maps even at the highest photon energy (33,keV) used in this study. Therefore, these results suggest that radiation damage in the energy range investigated could be evaluated based on absorbed dose without energy dependence, and that it is important to minimize the absorbed dose in a crystal sample for obtaining an accurate protein structure. [source] Crystal growth and structural refinement of NaMn7O12CRYSTAL RESEARCH AND TECHNOLOGY, Issue 10-11 2005E. Gilioli Abstract We report the crystal growth and the structural refinement of NaMn7O12, a manganite having a double perovskite structure. As in many similar compounds, there is coexistence of Mn3+ and Mn4+ but in this material they orderly occupy different sites for crystallographic reasons. Therefore, this peculiar structure can be considered as a model system for studying complex mechanisms such as charge, orbital and spin ordering. High purity bulk samples and "large" single crystals are needed to study tiny modifications in the crystallographic and magnetic structures associated to the ordering phenomena. Almost single phase (more than 96% pure) and single crystals (up to about 150 µm) of NaMn7O12 were synthesized by solid state reaction under pressure in a multi-anvil apparatus. Single crystal x-ray diffraction and SEM analysis have been used to characterize the crystals. The structure refinement indicates that NaMn7O12 crystallizes in the cubic Im3 space group, with a = 7.312 Å and Z = 2. Further studies are in progress to optimize the synthesis conditions, in order to grow larger crystals. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Cationic disorder, microstructure and dielectric response of ferroelectric SBT ceramicsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-2 2003Ch. Muller Polycrystalline samples of SrBi2Ta2O9 (acronym SBT) have been prepared by means of solid-state reaction either using a classical route or by mechanochemical activation. For each compound, a structural analysis of the ferroelectric orthorhombic phase (space group A21am) has been performed from the fitting of neutron and/or X-ray powder diffraction data using the Rietveld method. A cationic disorder on Bi3+ and Sr2+ crystallographic sites has been revealed, the Sr atoms occupying the Bi sites and vice versa. From diffraction peak broadening analyses of high-resolution synchrotron X-ray diffraction data, it has been shown that the two grinding methods (manual or mechanical) induce local strains, the average apparent strain being three times larger for the mechanically ground sample. In order to link microstructure and ferroelectric properties, the dielectric constant has been measured as a function of the temperature. It appears that the position and the shape of the dielectric anomaly strongly depend upon the composition and the route used to elaborate the powders. More exactly, for the mechanically ground powder, the large apparent strain, probably correlated to the strong cation exchange revealed by the structural refinement, leads to a significantly enhanced dielectric response. [source] Scaling of one-shot oscillation images with a reference data setJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004Kunio Hirata By combining a least-squares procedure with the program MOSFLM, a program SCLONE has been developed which processes diffraction images that do not contain serial oscillation images and may have a few or no full reflections. After each image was processed by MOSFLM, the partialities and structure amplitudes of the reflections were estimated using a least-squares method to refine the scaling factor, the relative temperature factor, the mosaic spread, cell constants, and missetting angles for each independent image. The SCLONE calculation significantly improved the quality of the intensities from the reflections obtained by the initial MOSFLM calculation and crystal structural refinement confirmed the improvement. The SCLONE calculation indicated that the reflection of the present crystal had a rocking curve that was steeper at the middle of the profile and more gradual at both ends of the profile than that assumed in the program MOSFLM. [source] Application of normal-mode refinement to X-ray crystal structures at the lower resolution limitACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Fengyun Ni The structural refinement of large complexes at the lower resolution limit is often difficult and inefficient owing to the limited number of reflections and the frequently high-level structural flexibility. A new normal-mode-based X-ray crystallographic refinement method has recently been developed that enables anisotropic B -factor refinement using a drastically smaller number of thermal parameters than even isotropic refinement. Here, the method has been systematically tested on a total of eight systems in the resolution range 3.0,3.9,Å. This series of tests established the most applicable scenarios for the method, the detailed procedures for its application and the degree of structural improvement. The results demonstrated substantial model improvement at the lower resolution limit, especially in cases in which other methods such as the translation,libration,screw (TLS) model were not applicable owing to the poorly converged isotropic B -factor distribution. It is expected that this normal-mode-based method will be a useful tool for structural refinement, in particular at the lower resolution limit, in the field of X-ray crystallography. [source] Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3,Å X-ray diffraction dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2008Eiji Nishibori Accurate structural refinement of a putative acylphosphatase using 1.3,Å X-ray diffraction data was carried out using charge densities determined by the maximum-entropy method (MEM). The MEM charge density clearly revealed detailed features of the solvent region of the putative acylphosphatase crystalline structure, some of which had never been observed in conventional Fourier maps. The structural model in the solvent region was constructed as distributions of anisotropic water atoms. The omit-difference MEM maps and the difference MEM maps were effective in revealing details of the protein structure, such as multiple conformations of the side chains of amino-acid residues, anisotropy of atoms and H atoms. By model building using the MEM charge densities, the reliability factors R1 and Rfree in the SHELX refinement were dramatically improved from 17.9% and 18.3% to 9.6% and 10.0%, respectively. The present results prove the usefulness of MEM in improving the accuracy of refinement of protein crystal structures. [source] Molecular Structure of ProlineCHEMISTRY - A EUROPEAN JOURNAL, Issue 18 2004Wesley D. Allen Dr. Abstract The molecular structures of the two lowest-energy conformers of proline, Pro- I and Pro- II, have been characterized by ab initio electronic structure computations. An extensive MP2/6-31G* quartic force field for Pro- I, containing 62,835 unique elements in the internal coordinate space, was computed to account for anharmonic vibrational effects, including total zero-point contributions to isotopomeric rotational constants. New re and improved r0 least-squares structural refinements were performed to determine the heavy-atom framework of Pro- I, based on experimentally measured (A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J. C. Lopez, J. L. Alonso, Angew. Chem.2002, 114, 4867; Angew. Chem. Int. Ed.2002, 41, 4673) rotational constant sets of nine isotopomers and our ab initio data for structural constraints and zero-point vibrational (ZPV) shifts. Without the ab initio constraints, even the extensive set of empirical rotational constants cannot satisfactorily fix the molecular structure of the most stable conformer of proline, a 17-atom molecule with no symmetry. After imposing the ab initio constraints, excellent agreement between theory and experiment is found for the heavy-atom geometric framework, the root-mean-square (rms) residual of the empirical rotational constant fit being cut in half by adding ZPV corrections. The most significant disparity, about 0.07 Å, between the empirical and the best ab initio structures, concerns the r(N,,,H) distance of the intramolecular hydrogen bond. Some of the experimental quartic centrifugal distortion constants assigned to Pro- II have been corrected based on data obtained from a theoretical force field. [source] | ||||||||||