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Crystallographic Unit Cell (crystallographic + unit_cell)
Selected AbstractsCation distribution in spinel (Mn,Co,Cr)3O4 at room temperatureJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2010A. Purwanto As part of a study of the long-term operation of solid-oxide fuel cells, three (Mn,Co,Cr)3O4 samples have been synthesized and characterized. X-ray and neutron diffraction patterns from the powder samples at room temperature were measured and the data were co-refined. The neutron data were indispensible in locating Mn, Co and Cr within the crystallographic unit cell with their respective atomic occupancies. Two of these samples have been identified as cubic Mn0.76Co0.58Cr1.66O4 and Mn1.28Co1.72O4. The third is a two-phase sample containing cubic Mn1.66Co1.34O4 and tetragonal Mn2.05Co0.91O4 in a 59.1,(6):40.9,(6)% mass fraction ratio. Cr, which might be introduced from reaction with chromia during oxidation of interconnect materials, exhibits a preference for the octahedral site rather than the tetrahedral site. Without Cr, Mn dominates the octahedral site. [source] Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sitesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2009Xinguo Hong Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the program GASBOR at 5,Å resolution (qmax = 1.25,Å,1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8,Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2, level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax = 0.25,Å,1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination of FSEARCH and WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement. [source] IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides.JOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2009Part III: comparison of solid state, solution structures of cyclo(L -Ser- L -Ser) Abstract B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L -Ser- L -Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L -seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol,1) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L -Ser- L -Ser), shows that the DKP ring displays a near-planar conformation, with both the two L -seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L -Ser- L -Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm,1, IR: 1666 and 1680 cm,1), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ,30 cm,1, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm,1. The occurrence of this cis amide II mode at a wavenumber above 1500 cm,1 concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C, atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd. [source] Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed formACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2004Gali Golan The Escherichia coli DNA repair enzyme endonuclease VIII (EndoVIII or Nei) excises oxidized pyrimidines from damaged DNA substrates. It overlaps in substrate specificity with endonuclease III and may serve as a back-up for this enzyme in E. coli. The three-dimensional structure of Nei covalently complexed with DNA has been recently determined, revealing the critical amino-acid residues required for DNA binding and catalytic activity. Based on this information, several site-specific mutants of the enzyme have been tested for activity against various substrates. Although the crystal structure of the DNA-bound enzyme has been fully determined, the important structure of the free enzyme has not previously been analyzed. In this report, the crystallization and preliminary crystallographic characterization of DNA-free Nei are described. Four different crystal habits are reported for wild-type Nei and two of its catalytic mutants. Despite being crystallized under different conditions, all habits belong to the same crystal form, with the same space group (I222) and a similar crystallographic unit cell (average parameters a = 57.7, b = 80.2, c = 169.7,Å). Two of these crystal habits, I and IV, appear to be suitable for full crystallographic analysis. Crystal habit I was obtained by vapour diffusion using PEG 8000, glycerol and calcium acetate. Crystal habit IV was obtained by a similar method using PEG 400 and magnesium chloride. Both crystals are mechanically strong and stable in the X-ray beam once frozen under cold nitrogen gas. A full diffraction data set has recently been collected from a wild-type Nei crystal of habit I (2.6,Å resolution, 85.2% completeness, Rmerge = 9.8%). Additional diffraction data were collected from an Nei-R252A crystal of habit IV (2.05,Å resolution, 99.9% completeness, Rmerge = 6.0%) and an Nei-E2A crystal of habit IV (2.25,Å resolution, 91.7% completeness, Rmerge = 6.2%). These diffraction data were collected at 95,100 K using a synchrotron X-ray source and a CCD area detector. All three data sets are currently being used to obtain crystallographic phasing via molecular-replacement techniques. [source] | ||||||||||