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Electron Density Maps (electron + density_map)
Selected AbstractsSynthesis and crystal structure of [CuCl(phen)2]3H3V10O28 · 7 H2OCRYSTAL RESEARCH AND TECHNOLOGY, Issue 7 2005E. Rakovský Abstract The new compound, [CuCl(phen)2]3H3V10O28 · 7 H2O, was prepared by reaction of an aqueous KVO3 solution (pH 3) with an aqueous solution of CuSO4 · 5 H2O in which 1,10-phenanthroline (phen) and KCl were added. The crystal structure of the compound was determined, and the proton position in H3V10O283, were calculated by the bond length/bond number method and also determined from difference electron density map. The protons are bound to colinearly arranged ,,OV2 and ,,OV3 groups which is the common protonation type in trihydrogen decavanadates. The structure crystallizes in P1 space group symmetry. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Advances in the free lunch methodJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2007Rocco Caliandro The most critical limit of macromolecular crystallography, the experimental data resolution, is partially `tricked' by the `free lunch method' (non-measured reflection extrapolation). The best electron density map available when only observed data are used may be employed to extrapolate moduli and phases of unobserved reflections behind and beyond the experimental resolution limit. The method is able to reduce the mean phase error of the observed reflections and to produce a more interpretable (in terms of a molecular model) electron density map. The main features of the free lunch method have been studied and its performance has been enhanced; it is beneficial even if data resolution is about 2,Å. Furthermore, the technique has been parameterized so that it may be routinely used by other phasing programs. [source] Long-range allosteric transitions in carbamoyl phosphate synthetasePROTEIN SCIENCE, Issue 9 2004James B. Thoden Abstract Carbamoyl phosphate synthetase plays a key role in both pyrimidine and arginine biosynthesis by catalyzing the production of carbamoyl phosphate from one molecule of bicarbonate, two molecules of MgATP, and one molecule of glutamine. The enzyme from Escherichia coli consists of two polypeptide chains referred to as the small and large subunits, which contain a total of three separate active sites that are connected by an intramolecular tunnel. The small subunit harbors one of these active sites and is responsible for the hydrolysis of glutamine to glutamate and ammonia. The large subunit binds the two required molecules of MgATP and is involved in assembling the final product. Compounds such as L-ornithine, UMP, and IMP allosterically regulate the enzyme. Here, we report the three-dimensional structure of a site-directed mutant protein of carbamoyl phosphate synthetase from E. coli, where Cys 248 in the small subunit was changed to an aspartate. This residue was targeted for a structural investigation because previous studies demonstrated that the partial glutaminase activity of the C248D mutant protein was increased 40-fold relative to the wild-type enzyme, whereas the formation of carbamoyl phosphate using glutamine as a nitrogen source was completely abolished. Remarkably, although Cys 248 in the small subunit is located at ,100 Å from the allosteric binding pocket in the large subunit, the electron density map clearly revealed the presence of UMP, although this ligand was never included in the purification or crystallization schemes. The manner in which UMP binds to carbamoyl phosphate synthetase is described. [source] Removing bias from solvent atoms in electron density mapsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2008Eric N. Brown Atomic structures of proteins determined via protein crystallography contain numerous solvent atoms. The experimental data for the determination of a water molecule's O-atom position is often a small contained blob of unidentified electron density. Unfortunately, the nature of crystallographic refinement lets poorly placed solvent atoms bias the future refined positions of all atoms in the crystal structure. This research article presents the technique of omit-maps applied to remove the bias introduced by poorly determined solvent atoms, enabling the identification of incorrectly placed water molecules in partially refined crystal structures. A total of 160 protein crystal structures with 45,912 distinct water molecules were processed using this technique. Most of the water molecules in the deposited structures were well justified. However, a few of the solvent atoms in this test data set changed appreciably in position, displacement parameter or electron density when fitted to the solvent omit-map, raising questions about how much experimental support exists for these solvent atoms. [source] The revenge of the Patterson methods.JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2007The Patterson techniques, recently developed by the same authors for the ab initio crystal structure solution of proteins, have been applied to single and multiple anomalous diffraction (SAD and MAD) data to find the substructure of the anomalous scatterers. An automatic procedure has been applied to a large set of test structures, some of which were originally solved with remarkable difficulty. In all cases, the procedure automatically leads to interpretable electron density maps. Patterson techniques have been compared with direct methods; the former seem to be more efficient than the latter, so confirming the results obtained for ab initio phasing, and disproving the common belief that they could only be applied to determine large equal-atom substructures with difficulty. [source] Quantum chemical geometry optimizations in proteins using crystallographic raw dataJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2002Ulf Ryde Abstract A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N -methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4,6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1058,1070, 2002 [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] Lattice dynamics of chalcopyrite semiconductors LiAlTe2, LiGaTe2 and LiInTe2PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2009A. V. Kosobutsky Abstract Within density functional perturbation theory using norm-conserving pseudopotentials and a plane-wave basis set calculations of phonon dispersion relations and densities of states of LiAlTe2, LiGaTe2 and LiInTe2 compounds being crystallized into the tetragonal chalcopyrite structure have been performed. Theoretical values of phonon mode frequencies in LiGaTe2 and LiInTe2 are in good agreement with the experimental data available for these crystals obtained by the methods of Raman and infrared spectroscopies. The similarity of the physical and chemical properties of the crystals concerned manifests itself in the similarity of their phonon spectra that are especially close to each other in low- and high-frequency ranges. Phonon modes of the upper phonon band are predominantly caused by the lithium sublattice vibrations and have an upper bound of 350,370 cm,1. In a mid-frequency range a significant downshift of the vibrational frequencies is observed on going from LiAlTe2 to LiGaTe2 and LiInTe2 that is a consequence of the third group cation mass reduction. From calculated electron density maps it follows that Li-containing chalcopyrites are characterized by a less pronounced bond between the first group cation and anion as compared with the Cu- and Ag-based analogs due to the absence of pd-hybridization. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] | |||||||||||||