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Difference Fourier Maps (difference + fourier_map)
Selected AbstractsThe (Fo,Fc) Fourier synthesis: a probabilistic studyACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2008Rocco Caliandro (Fo,Fc) and (2Fo,Fc) Fourier syntheses are considered the most powerful tools for recovering the remainder of a structure and for correcting crystal structure models. A probabilistic approach has been applied to derive the formula for the variance for the expected value of the coefficient (Fo,Fc). This has allowed a better understanding of the features of the difference Fourier synthesis; in particular, a subset of well phased reflections has been separated from the subset of reflections best phased by the standard Fo Fourier synthesis. An iterative procedure, based on the electron-density modification of the difference Fourier map, has been devised which aims to improve phase and modulus estimates of the reflections with higher variance value, by using as lever arm the set of reflections with lower variance value. The new procedure (DEDM) has been implemented and verified on a wide set of test structures, the partial models of which were obtained by molecular replacement or by automatic model-building routines applied to experimental electron-density maps. Phase and modulus estimates of the difference Fourier syntheses improve in all the test cases; as a consequence, the quality of the difference Fourier maps also improves in the region where the target structure deviates from the partial model. A new procedure is suggested, combining DEDM with standard electron-density modification techniques, which leads to significant reduction of the phase errors. The procedure may be considered a starting point for further developments. [source] Structure of lithium benzilate hemihydrate solved by simulated annealing and difference Fourier synthesis from powder dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2003Asiloé J. Mora The crystal structure of lithium benzilate hemihydrate (C14H11OLi+·0.5H2O) was solved from synchrotron powder diffraction data. This compound crystallizes in the monoclinic space group P21/a. The structure was solved via the direct space search for two benzilate fragments using the simulated-annealing program DASH, localization of the lithium ions and water molecule from a difference Fourier map, and a restrained Rietveld refinement (Rwp = 0.0687). The structure is a coordination polymer of [Li2(C14H11O3)2·H2O]2 tetramers building helical fourfold one-dimensional channels parallel to [010]. Inside the channels the tetrahedral coordination spheres of the lithium ions contain hydroxyl and carbonyl groups, and water molecules. The water molecule functions as the cohesive entity forming extended hydrogen-bonded chains running along [010], and bifurcated donor hydrogen bonds with the two nearest carboxylates. At the outer edge of the channels, weaker intermolecular C,H,Ph hydrogen bonds along [100] and [001] contribute to the supramolecular aggregation of the structure. [source] A description of the structural determination procedures of a gap junction channel at 3.5,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009Michihiro Suga Intercellular signalling is an essential characteristic of multicellular organisms. Gap junctions, which consist of arrays of intercellular channels, permit the exchange of ions and small molecules between adjacent cells. Here, the structural determination of a gap junction channel composed of connexin 26 (Cx26) at 3.5,Å resolution is described. During each step of the purification process, the protein was examined using electron microscopy and/or dynamic light scattering. Dehydration of the crystals improved the resolution limits. Phase refinement using multi-crystal averaging in conjunction with noncrystallographic symmetry averaging based on strictly determined noncrystallographic symmetry operators resulted in an electron-density map for model building. The amino-acid sequence of a protomer structure consisting of the amino-terminal helix, four transmembrane helices and two extracellular loops was assigned to the electron-density map. The amino-acid assignment was confirmed using six selenomethionine (SeMet) sites in the difference Fourier map of the SeMet derivative and three intramolecular disulfide bonds in the anomalous difference Fourier map of the native crystal. [source] Use of Cr K, radiation to enhance the signal from anomalous scatterers including sulfurJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-2 2000Witek Kwiatkowski The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the Cr K, radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the Cu K, and Cr K, data were similar but better than that for Au L,. This result was in spite of the fourfold higher flux from the Cu anode versus the Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the Cr K, data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the Au L, data. The ability to enhance the S-derived anomalous signal using Cr K, radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the Cr K, data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method. [source] The Crystal Structure of the L1 Intermediate of Halorhodopsin at 1.9 Å Resolution,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2007Walter Gmelin The mutant T203V of the light driven chloride pump halorhodopsin from Halobacterium salinarum was crystallized and the X-ray structure was solved at 1.6 Å resolution. The T203V structure turned out to be nearly identical to the wild type protein with a root mean square deviation of 0.43 Å for the carbon , atoms of the protein backbone. Two chloride binding (CB) sites were demonstrated by a substitution of chloride with bromide and an analysis of anomalous difference Fourier maps. The CB1 site was found at the same position as in the wild type structure. In addition, a second chloride binding site CB2 was identified around Q105 due to higher resolution in the mutant crystal. As T203V showed a 10 times slower decay of its photocycle intermediate L, this intermediate could be trapped with an occupancy of 60% upon illumination at room temperature and subsequent cooling to 120°K. Fourier transform infrared spectroscopy clearly identified the crystal to be trapped in the L1 intermediate state and the X-ray structure was solved to 1.9 Å resolution. In this intermediate, the chloride moved by 0.3 Å within binding site CB1 as indicated by peaks in difference Fourier density maps. The chloride in the second binding site CB2 remained unchanged. Thus, intraproteinous chloride translocation from the extracellular to the cytoplasmic part of the protein must occur in reaction steps following the L1 intermediate in the catalytic cycle of halorhodopsin. [source] Determination 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] Twinning and structure of Eu0.6Sr0.4MnO3ACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2006Nicola Rotiroti The crystal structure of europium strontium manganese trioxide, Eu0.6Sr0.4MnO3, has been refined using a multiply twinned single crystal containing six twin components. The MnO6 octahedra show Jahn,Teller distortions with nearly fourfold symmetry, but the octahedral tilting scheme reduces the crystal symmetry to orthorhombic (space group Pbnm). The refinement of site occupancies and the analysis of difference Fourier maps show that the Eu3+ and Sr2+ cations occupy different crystallographic positions with eightfold and twelvefold coordination, respectively. [source] The Stuffed Framework Structure of SrP2N4: Challenges to Synthesis and Crystal Structure DeterminationCHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2007Friedrich Abstract SrP2N4 was obtained by high-pressure high-temperature synthesis utilizing the multianvil technique (5,GPa, 1400,°C) starting from mixtures of phosphorus(V) nitride and strontium azide. SrP2N4 turned out to be isotypic with BaGa2O4 and is closely related to KGeAlO4. The crystal structure (SrP2N4, a=17.1029(8), c=8.10318(5),Å, space group P63 (no. 173), V=2052.70(2),Å3, Z=24, R(F2)=0.0633) was solved from synchrotron powder diffraction data by applying a combination of direct methods, Patterson syntheses, and difference Fourier maps adding the unit cell information derived from electron diffraction and symmetry information obtained from 31P solid-state NMR spectroscopy. The structure of SrP2N4 was refined by the Rietveld method by utilizing both neutron and synchrotron X-ray powder diffraction data, and has been corroborated additionally by 31P solid-state NMR spectroscopy by employing through-bond connectivities and distance relations. [source] | ||||||||||