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Unit-cell Volume (unit-cell + volume)
Selected AbstractsHigh-resolution synchrotron radiation studies on natural and thermally annealed scleractinian coral biomineralsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2007J. Stolarski The structural phase transition from aragonite to calcite in biogenic samples extracted from the skeletons of selected scleractinian corals has been studied by synchrotron radiation diffraction. Biogenic aragonite samples were extracted en bloc without pulverization from two ecologically different scleractinian taxa: Desmophyllum (deep-water, solitary and azooxanthellate) and Favia (shallow-water, colonial, zooxanthellate). It was found that natural (not pulverized) samples contribute to narrow Bragg peaks with ,d/d values as low as 1 × 10,3, which allows the exploitation of the high resolution of synchrotron radiation diffraction. A precise determination of the lattice parameters of biogenic scleractinian coral aragonite shows the same type of changes of the a, b, c lattice parameter ratios as that reported for aragonite extracted from other invertebrates [Pokroy, Quintana, Caspi, Berner & Zolotoyabko (2004). Nat. Mater.3, 900,902]. It is believed that the crystal structure of biogenic samples is influenced by interactions with organic molecules that are initially present in the biomineralization hydrogel. The calcite phase obtained by annealing the coral samples has a considerably different unit-cell volume and lattice parameter ratio c/a as compared with reference geological calcite and annealed synthetic aragonite. The internal strain in the calcite structure obtained by thermal annealing of the biomineral samples is about two times larger than that found in the natural aragonite structure. This effect is observed despite slow heating and cooling of the sample. [source] Atomic displacements at and order of all phase transitions in multiferroic YMnO3 and BaTiO3ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2009S. C. Abrahams Coordinate analysis of the multiple phase transitions in hexagonal YMnO3 leads to the prediction of a previously unknown aristotype phase, with the resulting phase-transition sequence: P63,cm,(e.g.) ,P63cm,P63/mcm,P63/mmc,P6/mmm. Below the Néel temperature TN, 75,K, the structure is antiferromagnetic with the magnetic symmetry not yet determined. Above TN the P63cm phase is ferroelectric with Curie temperature TC, 1105,K. The nonpolar paramagnetic phase stable between TC and ,,1360,K transforms to a second nonpolar paramagnetic phase stable to ,,1600,K, with unit-cell volume one-third that below 1360,K. The predicted aristotype phase at the highest temperature is nonpolar and paramagnetic, with unit-cell volume reduced by a further factor of 2. Coordinate analysis of the three well known phase transitions undergone by tetragonal BaTiO3, with space-group sequence R3m,Amm2 ,P4mm,Pmm, provides a basis for deriving the aristotype phase in YMnO3. Landau theory allows the I , II, III , IV and IV , V phase transitions in YMnO3, and also the I , II phase transition in BaTiO3, to be continuous; all four, however, unambiguously exhibit first-order characteristics. The origin of phase transitions, permitted by theory to be second order, that are first order instead have not yet been thoroughly investigated; several possibilities are briefly considered. [source] Characterization of the pressure-induced second-order phase transition in the mixed-valence vanadate BaV6O11ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009Karen Friese The pressure dependence of the structure of the mixed-valence vanadate BaV6O11 was studied with single-crystal X-ray diffraction in a diamond,anvil cell. The compressibility data could be fitted with a Murnaghan equation of state with the zero-pressure bulk modulus B0 = 161,(7),GPa and the unit-cell volume at ambient pressure = 387.1,(3),Å (B, = 4.00). A phase transition involving a symmetry reduction from P63/mmc to P63mc can be reliably detected in the high-pressure data. The estimated transition pressure lies in the range 1.18,<,Pc,<,3.09,GPa. The transition leads to a breaking of the regular Kagomé net formed by part of the V ions. While in the ambient pressure structure all V,V distances in the Kagomé net are equal, they split into inter-trimer and intra-trimer distances in the high-pressure phase. In general, these changes are comparable to those observed in the corresponding low-temperature transition. However, the pressure-induced transition takes place at a lower unit-cell volume compared with the temperature-induced transition. Furthermore, overall trends for inter-trimer and intra-trimer V,V distances as a function of the unit-cell volume are clearly different for datapoints obtained by variation of pressure and temperature. The behavior of BaV6O11 is compared with that of NaV6O11. While in the latter compound the transition can be explained as a pure volume effect, in BaV6O11 an additional degree of freedom related to the valence distribution among the symmetrically independent vanadium sites has to be taken into account. [source] DIBER: protein, DNA or both?ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Grzegorz Chojnowski The program DIBER (an acronym for DNA and FIBER) requires only native diffraction data to predict whether a crystal contains protein, B-form DNA or both. In standalone mode, the classification is based on the cube root of the reciprocal unit-cell volume and the largest local average of diffraction intensities at 3.4,Å resolution. In combined mode, the Phaser rotation-function score (for the 3.4,Å shell and a canonical B-DNA search model) is also taken into account. In standalone (combined) mode, DIBER classifies 87.4 ± 0.2% (90.2 ± 0.3%) of protein, 69.1 ± 0.3% (78.8 ± 0.3%) of protein,DNA and 92.7 ± 0.2% (90.0 ± 0.2%) of DNA crystals correctly. Reliable predictions with a correct classification rate above 80% are possible for 36.8 ± 1.0% (60.2 ± 0.4%) of the protein, 43.6 ± 0.5% (59.8 ± 0.3%) of the protein,DNA and 83.3 ± 0.3% (82.6 ± 0.4%) of the DNA structures. Surprisingly, selective use of the diffraction data in the 3.4,Å shell improves the overall success rate of the combined-mode classification. An open-source CCP4/CCP4i -compatible version of DIBER is available from the authors' website at http://www.iimcb.gov.pl/diber and is subject to the GNU Public License. [source] Soaking: the effect of osmotic shock on tetragonal lysozyme crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2002F. J. López-Jaramillo Protein crystals crack when they are soaked in a solution with ionic strength sufficiently different from the environment in which they grew. It is demonstrated for the case of tetragonal lysozyme that the forces involved and the mechanisms that lead to the formation of cracks are different for hypertonic and hypotonic soaking. Tetragonal lysozyme crystals are very sensitive to hypotonic shocks and, after a certain waiting time, cracks always appear with a characteristic pattern perpendicular to the crystallographic c axis. Conversely, a hypertonic shock is better withstood: cracks do not display any deterministic pattern, are only visible at higher differences in ionic strength and after a certain time a phenomenon of crystal reconstruction occurs and the cracks vanish. At the lattice level, the unit-cell volume expands in hypotonic shock and shrinks under hypertonic conditions. However, the compression of the unit cell is anisotropic: the c axis is compressed to a minimum, beyond which it expands despite the unit-cell volume continuing to shrink. This behaviour is a direct consequence of the positive charge that the crystals bear and the existence of channels along the crystallographic c axis. Both features are responsible for the Gibbs,Donnan effect which limits the free exchange of ions and affects the movement of water inside the channels and bound to the protein. [source] The protein content in crystals and packing coefficients in different space groupsACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2000Klas M. Andersson A precise way of estimating the packing coefficient, i.e. the ratio between the protein and unit-cell volume, or solvent content in protein crystals is given. At present, the solvent content is not given for most proteins in the Protein Data Bank and in many cases where it is given the values are dubious. The mean density of proteins in the crystalline form is around 1.22,g,cm,3, not 1.35,g,cm,3 as usually stated. This is equivalent to 19.5,Å3 per non-H atom. A statistical investigation of the average protein content and packing coefficient in different space groups is presented. The packing coefficients are generally higher in the most frequently occurring space groups than in the uncommon space groups. There is also a remarkable difference in frequency distribution for enantiomorphous pairs of space groups. [source] Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2,,-phosphotransferase-IVaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Marta Toth The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2,,-phosphotransferase-IVa [APH(2,,)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, although one of the crystal forms had a unit-cell volume that was approximately 13% smaller than the other and a very low solvent content of around 38%. The third crystal form belonged to the monoclinic space group P21 and preliminary X-ray diffraction analysis was consistent with the presence of two molecules in the asymmetric unit. The orthorhombic crystal forms of apo APH(2,,)-IVa both diffracted to 2.2,Å resolution and the monoclinic crystal form diffracted to 2.4,Å resolution; synchrotron diffraction data were collected from these crystals at SSRL (Stanford, California, USA). Structure determination by molecular replacement using the structure of the related enzyme APH(2,,)-IIa is proceeding. [source] Aplanarity of CO3 groups: a theoretical investigationACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2000Björn Winkler Density functional theory-based calculations have been used to demonstrate that the aplanarity of CO groups in some carbonates such as dolomite, CaMg(CO), aragonite, CaCO, and norsethite, BaMg(CO), is a ground-state property. This distortion stabilizes dolomite by ,500,J,mol. Up to at least 6,GPa, the aplanarity of CO groups in dolomite is independent of pressure. In aragonite the aplanarity increases slightly on increasing pressure, while a significant tilting of the CO groups occurs. The calculations do not support previous findings of anomalously low values for the pressure derivative of the bulk moduli, , of aragonite and dolomite. Instead, the computed pressure dependences of the unit-cell volumes correspond to = 5.0,(5) for aragonite and = 4,(1) for dolomite, when fitted with a third-order Birch,Murnaghan equation-of-state. [source] A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2006Monika Budayova-Spano Crystallization and preliminary neutron diffraction measurements of rasburicase, a recombinant urate oxidase enzyme expressed by a genetically modified Saccharomyces cerevisiae strain, complexed with a purine-type inhibitor (8-azaxanthin) are reported. Neutron Laue diffraction data were collected to 2.1,Å resolution using the LADI instrument from a crystal (grown in D2O) with volume 1.8,mm3. The aim of this neutron diffraction study is to determine the protonation states of the inhibitor and residues within the active site. This will lead to improved comprehension of the enzymatic mechanism of this important enzyme, which is used as a protein drug to reduce toxic uric acid accumulation during chemotherapy. This paper illustrates the high quality of the neutron diffraction data collected, which are suitable for high-resolution structural analysis. In comparison with other neutron protein crystallography studies to date in which a hydrogenated protein has been used, the volume of the crystal was relatively small and yet the data still extend to high resolution. Furthermore, urate oxidase has one of the largest primitive unit-cell volumes (space group I222, unit-cell parameters a = 80, b = 96, c = 106,Å) and molecular weights (135,kDa for the homotetramer) so far successfully studied with neutrons. [source] | ||||||||||