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Different Crystals (different + crystal)
Terms modified by Different Crystals Selected AbstractsThe structure of orange HgI2.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2002The metastable orange crystals of HgI comprise three different crystal structures all of which are built from corner-linked HgI supertetrahedra. Two of the structures are end members with the maximum degree of order (MDO) of a polytypic layer structure. In this paper, the third structure (D) determined from X-ray diffraction, a crystal chemical discussion of the four known tetrahedral HgI structures, and a twinning model are presented. All the various diffraction results published during the past 70 years are now explained. The HgI supertetrahedra of the tetragonal structure D are corner-linked into two interpenetrating diamond-type networks. The stable red form and the three orange structures show the same cubic densest packing of I atoms and differ only in the distribution of Hg atoms in the tetrahedral voids. Transformations between the structures may involve only movements of Hg atoms, as implied by larger thermal displacement parameters of Hg than of I. A multiply twinned conglomerate of MDO1, MDO2 and D, each structure occurring in three orientations, results in metrically cubic crystals whose Bragg reflections are very close to reciprocal lattice points. [source] X-ray absorption by macromolecular crystals: the effects of wavelength and crystal composition on absorbed doseJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2004James W. Murray Radiation damage restricts the useful lifetime for macromolecular crystals in the X-ray beam, even at cryotemperatures. With the development of structural genomics pipelines, it will be essential to incorporate projected crystal lifetime information into the automated data collection software routines. As a first step towards this goal, a computer program, RADDOSE, is presented which is designed for use by crystallographers in optimizing the amount of data that can be obtained from a particular cryo-cooled crystal at synchrotron beamlines. The program uses the composition of the crystal and buffer constituents, as well as the beam energy, flux and dimensions, to compute the absorption coefficients and hence the theoretical time taken to reach an absorbed dose of 2,×,,Gy, the so-called `Henderson limit'. At this dose, the intensity of the diffraction pattern is predicted to be halved. A `diffraction,dose efficiency' quantity is introduced, for the convenient comparison of absorbed dose per diffracted photon for different crystals. Four example cases are considered, and the implications for anomalous data collection are discussed in the light of the results from RADDOSE. [source] Calculation of XANES/ELNES Spectra of All Edges in Si3N4 and Si2N2OJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 1 2002Wai-Yim Ching Using a recently developed first-principles supercell method that includes the electron and core-hole interaction, the XANES/ELNES spectra of Si- L2,3, Si- K, and N- K edges in ,-Si3N4, ,-Si3N4, spinel c -Si3N4, and Si2N2O were calculated and compared. The difference in total energies between the initial ground state and the final core-hole state provides the transition energy. The calculated spectra are found to be in good agreement with the experimental measurements on ,-Si3N4 and c -Si3N4. The differences in the XANES/ELNES spectra for the same element in different crystals are explained in terms of differences in local bonding. The use of orbital-decomposed local density of states to explain the measured spectra is shown to be inadequate. These results reaffirm the importance of including the core-hole effect in any XANES/ELNES spectral calculation. [source] Structures of the OmpF porin crystallized in the presence of foscholine-12PROTEIN SCIENCE, Issue 5 2010Georgia Kefala Abstract The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 Å, b = 210.5 Å, c = 137 Å, and , = 100.5°, and the resolution of 3.8 Å. The second structure was solved at the resolution of 4.4 Å and was refined in the P321 space group, with unit cell parameters a = 215.5 Å, b = 215.5 Å, c = 137.5 Å, and , = 120°. Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli. [source] Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Jeanette Netzel Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T, 20,K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (lmax = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C,C, C,N and C,O bonds, and for hydrogen bonds together with covalent C,H and N,H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. [source] A novel method of determining the number of macromolecules per asymmetric unit from accurate crystal-volume measurementsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2003Fang Li Knowledge of the number of macromolecules per crystallographic asymmetric unit is frequently useful in the determination of crystal structures. A method has been developed to establish this number directly from measurements of the volume and macromolecular contents of a crystal. The volume of a crystal is determined by measuring the volume of solvent that it displaces in a fine capillary tube. The macromolecular mass contained in a crystal is measured by dissolving the crystal in a known amount of water or suitable buffer and then measuring the UV absorbance of the solution. The method has been tested successfully on three different crystals of known structures. [source] Crystallization and preliminary X-ray analysis of the human vascular adhesion protein-1ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003Yvonne Nymalm Human vascular adhesion protein-1 (VAP-1) is a membrane-bound multifunctional glycoprotein with both adhesive and enzymatic properties. The protein belongs to the copper-containing amine oxidase (CAO) family, which use 2,4,5-trihydroxyphenylalanine quinone as a cofactor. Here, the crystallization and preliminary X-ray analysis of a mammalian CAO, human VAP-1, is reported. The protein was expressed in Chinese hamster ovary cells as a full-length form with an N-terminal transmembrane region and multiple glycosylation sites. Hexagonal crystals with unit-cell parameters a = b = 225.9, c = 218.7,Å, , = , = 90, , = 120° were obtained using the vapour-diffusion method. Data from three different crystals were collected at 100,K using synchrotron radiation and were processed to 3.2,Å resolution with 95.9% completeness and an Rmerge of 19.6%. [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] Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2,-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001Masaru Tsunoda To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2,-deoxy-5-formyluridine at X, were obtained under several conditions with and without divalent cations. The crystal structures are all isomorphous. The octahedrally hydrated magnesium cations found in the major groove cement the two neighbouring duplexes along the b axis. In the Mg2+ -free crystals, a five-membered ring of water molecules occupies the same position as the magnesium site and connects the two duplexes similarly to the hydrated Mg2+ ion. It has been concluded that water molecules can take the place of the hydrated magnesium cation in crystallization, but the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution. In all four crystals, the 5-formyluracil residues form the canonical Watson,Crick pair with adenine residues. [source] | ||||||||||