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Temperature Factors (temperature + factor)
Kinds of Temperature Factors Selected AbstractsScaling of one-shot oscillation images with a reference data setJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004Kunio Hirata By combining a least-squares procedure with the program MOSFLM, a program SCLONE has been developed which processes diffraction images that do not contain serial oscillation images and may have a few or no full reflections. After each image was processed by MOSFLM, the partialities and structure amplitudes of the reflections were estimated using a least-squares method to refine the scaling factor, the relative temperature factor, the mosaic spread, cell constants, and missetting angles for each independent image. The SCLONE calculation significantly improved the quality of the intensities from the reflections obtained by the initial MOSFLM calculation and crystal structural refinement confirmed the improvement. The SCLONE calculation indicated that the reflection of the present crystal had a rocking curve that was steeper at the middle of the profile and more gradual at both ends of the profile than that assumed in the program MOSFLM. [source] Evaluation of soil saturation, soil chemistry, and early spring soil and air temperatures as risk factors in yellow-cedar declineGLOBAL CHANGE BIOLOGY, Issue 3 2006D. V. D'AMORE Abstract Yellow-cedar (Callitropsis nootkatensis (D. Don) Oerst.) is a valuable tree species that is experiencing a widespread decline and mortality in southeast Alaska. This study evaluated the relative importance of several potential risk factors associated with yellow-cedar decline: soil saturation, soil aluminum (Al) toxicity or calcium (Ca) deficiency, and air and soil temperature. Data were collected from permanent vegetation plots established in two low-elevation coastal forests exhibiting broad ranges of cedar mortality. Measurements of each risk factor were contrasted among classified forest zones to indicate if there were strong links with decline. Hydrology alone is weakly associated with yellow-cedar decline, but could have a predisposing role in the decline by creating exposed conditions because of reduced forest productivity. Yellow-cedar decline is not strongly associated with soil pH and extractable Al and Ca, but there appears to be Ca enrichment of surface soils by feedback from dead yellow-cedar foliage. Air and soil temperature factors are strongly associated with decline. Based on these results, an hypothesis is presented to explain the mechanism of tree injury where exposure-driven tree mortality is initiated in gaps created by soil saturation and then expands in gaps created by the tree-mortality itself. The exposure allows soils to warm in early spring causing premature dehardening in yellow-cedar trees and subsequent freezing injury during cold events. Yellow-cedars growing in the protection of shade or snow are not preconditioned by this warming, and thus not as susceptible to cold injury. Yellow-cedar decline appears to be associated with regional climate changes, but whether the cause of these changes is related to natural or human-induced climate shifts remains uncertain. Management implications, the possible role of climate, and recommended research are discussed. [source] Identification of bound waters in the solution structure of ribonuclease T1 using the double pulsed field gradient spin-echo NMR technique for selective water excitationMAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2002Mitsuru Tashiro Abstract Novel pulse sequences incorporating the double pulsed field gradient spin-echo technique are presented that have particular use in identifying macromolecular bound water. The use of these sequences is illustrated using ribonuclease T1. Five amide protons cross-relaxing with bound water protons were observed. Examination of the crystal structure revealed that all of these amide protons donate hydrogen bonds or are in close proximity to water molecules with very low temperature factors, indicating that these amide protons are highly correlated with the bound water molecules. This method rapidly provides reliable information for characterizing macromolecular bound water molecules. Copyright © 2002 John Wiley & Sons, Ltd. [source] Intersubsystem chemical bonds in the misfit layer compounds (LaS)1.13TaS2 and (LaS)1.14NbS2ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2002Andreas Jobst The modulated structures of incommensurate composite crystals (La0.912S)1.13TaS2 at room temperature and of (La0.949S)1.14NbS2 at T = 115,K are refined against high-resolution X-ray data. The compounds are isostructural with superspace group F,m2m(,,0,0)00s. For (LaS)1.13TaS2, lattice parameters of the first subsystem TaS2 were obtained as a = 3.2922,(1), b = 5.7776,(2) and c = 23.013,(2),Å. For the second subsystem LaS, the same b and c parameters were found, but a = 5.8090,(8),Å. Refinements led to a final structure model with R = 0.036 for 4767 observed unique reflections (R = 0.023 for 2147 main reflections, R = 0.099 for 1554 first-order satellites and R = 0.112 for 1042 second-order satellites). The final model includes modulation parameters up to the second-order harmonics for the displacements of the atoms, for the occupational parameters and for the temperature parameters. A clear correlation is found between the relative positions of the subsystems, the displacement modulation, the occupational modulation and the modulation of the temperature parameters. The analysis shows that the variations in environments are resolved by correlated variations in the temperature factors. For (LaS)1.14NbS2, lattice parameters at T = 115,K of the NbS2 subsystem were obtained as a = 3.3065,(4), b = 5.7960,(5) and c = 22.956,(3),Å. For the LaS subsystem, the same values for b and c were obtained, but a = 5.7983,(7),Å. Refinements led to a final structure model with R = 0.048 for 5909 observed unique reflections (R = 0.034 for 2528 main reflections, R = 0.092 for 2171 first-order satellites and R = 0.113 for 1103 second-order satellites). The final structure model is similar to that of (LaS)1.13TaS2. In particular, it is found that the values of the modulation parameters are almost equal and it is concluded that the modulations are independent of the temperature and the replacement of Ta with Nb, and thus represent a general mechanism of resolving the strain between the mutually incommensurate layers. [source] Structural basis for the phase transitions of Cs2HgCl4ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Bagautdin Bagautdinov The a0× b0× 2c0 twofold superstructure of dicaesium mercury tetrachloride, Cs2HgCl4, at T = 120,K has been determined by single-crystal X-ray diffraction using synchrotron radiation. Lattice parameters were found as a = 9.7105,(2), b = 7.4691 (1), c = 26.8992 (4) Å, and , = 90.368,(1)° with the supercell space group P21/c. Refinements on 1828 observed unique reflections converged to R = 0.053 (wR = 0.057) using anisotropic temperature factors for all atoms. This phase is the stable phase of Cs2HgCl4 below 163,K. A quantitative comparison is made of the distortions of the 2c0 superstructure with the undistorted phase that is stable at room temperature, and with the 3c0 and 5a0 superstructures that are stable at temperatures between 163,K and room temperature. The principal difference between the 2c0 superstructure and all other phases of Cs2HgCl4 is that the Cs cations are displaced away from the centers of their coordination polyhedra in the 2c0 superstructure. The structural basis for the driving force of the series of phase transitions in this compound is found in the variations of the environments of Cs atoms and in the variations of the distortions of the HgCl4 tetrahedra. [source] Structure, phase transitions and ionic conductivity of K3NdSi6O15·xH2O.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000-K3NdSi6O15·2H2O, its polymorphs Hydrothermally grown crystals of ,-K3NdSi6O15·2H2O, potassium neodymium silicate, have been studied by single-crystal X-ray methods. The compound crystallizes in space group Pbam, contains four formula units per unit cell and has lattice constants a = 16.008,(2), b = 15.004,(2) and c = 7.2794,(7),Å, giving a calculated density of 2.683,Mg,m,3. Refinement was carried out with 2161 independent structure factors to a residual, R(F), of 0.0528 [wR(F2) = 0.1562] using anisotropic temperature factors for all atoms other than those associated with water molecules. The structure is based on highly corrugated (Si2O52,), layers which can be generated by the condensation of xonotlite-like ribbons, which can, in turn, be generated by the condensation of wollastonite-like chains. The silicate layers are connected by Nd octahedra to form a three-dimensional framework. Potassium ions and water molecules are located in interstitial sites within this framework, in particular, within channels that extend along [001]. Aging of as-grown crystals at room temperature for periods of six months or more results in an ordering phenomenon that causes the length of the c axis to double. In addition, two phase transitions were found to occur upon heating. The high-temperature transformations, investigated by differential scanning calorimetry, thermal gravimetric analysis and high-temperature X-ray diffraction, are reversible, suggesting displacive transformations in which the layers remain intact. Conductivity measurements along all three crystallographic axes showed the conductivity to be greatest along [001] and further suggest that the channels present in the room-temperature structure are preserved at high temperatures so as to serve as pathways for easy ion transport. Ion-exchange experiments revealed that silver can readily be incorporated into the structure. [source] Structure, phase transitions and ionic conductivity of K3NdSi6O15·xH2O.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000Hydrothermally grown crystals of ,-K3NdSi6O15, potassium neodymium silicate, have been studied by single-crystal X-ray methods. Under appropriate conditions, the compound crystallizes in space group Bb21m and has lattice constants a = 14.370,(2), b = 15.518,(2) and c = 14.265,(2),Å. There are 30 atom sites in the asymmetric unit of the basic structure. With eight formula units per unit cell, the calculated density is 2.798,Mg,m,3. Refinement was carried out to a residual, wR(F2), of 0.1177 [R(F) = 0.0416] using anisotropic temperature factors for all atoms. The structure is based on (Si2O52,), layers, connected by Nd polyhedra to form a three-dimensional framework. Potassium ion sites, some of which are only partially occupied, are located within channels that run between the silicate layers. The silica,neodymia framework of ,-K3NdSi6O15, in particular the linkages formed between the silicate layers and Nd polyhedra, bears some similarities to that of the essentially isocompositional phase ,-K3NdSi6O15·2H2O. In both, the silicate layers are corrugated so as to accommodate a simple cubic array of NdO6 octahedra with lattice constant , 7.5,Å. Furthermore, the Si2O5 layers in ,-K3NdSi6O15 are topologically identical to those of the mineral sazhinite, Na2HCeSi6O15. Although ,-K3NdSi6O15 and sazhinite are not isostructural, the structures of each can be described as slight distortions of a high-symmetry parent structure with space group Pbmm. [source] Iodide-SAD, SIR and SIRAS phasing for structure solution of a nucleosome assembly proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Manickam Yogavel The crystal structure of Plasmodium falciparum nucleosome assembly protein (PfNapL) was determined by iodide-SAD/SIRAS phasing methods using iodide-SAD data to 3.0,Å resolution and native data to 2.4,Å resolution. Halide-derivatized PfNapL crystals were obtained using the quick cryo-soaking method in which the native crystals were soaked in a cryosolution consisting of 500,mM NaI for a short period of 30,60,s and data were collected at an in-house X-ray source using Cu,K, radiation. Despite a low anomalous signal-to-noise ratio of <1.2 in the >3.5,Å resolution bin, the data were sufficient to determine the structure by SAD/SIR/SIRAS methods using the soaked iodides. Previously, structure solution had failed with both molecular-replacement and selenomethionine-derivatization techniques owing to reasons that are detailed in this work. The phasing at low resolution with three iodides per monomer with high temperature factors was successful using any of the SAD, SIR or SIRAS methods. [source] A comparison of refined X-ray structures of hydrogenated and perdeuterated rat ,E-crystallin in H2O and D2OACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2005Jean-Baptiste Artero Rat ,E-crystallin was overexpressed, purified under different labelling conditions and crystallized and X-ray data were collected at resolutions between 1.71 and 1.36,Å. The structures were determined by molecular replacement. In these structures, the cd loop of the Greek-key motif 3, which is the major structural key motif of the two phase-transition groups of ,-crystallins, presents a double conformation. The influence of the perdeuteration on the protein structure was determined by comparison of the atomic positions and temperature factors of the different models. The perdeuterated proteins have a similar structure to their hydrogenated counterparts, but partial or full deuteration may have some effect on the atomic B -factor values. [source] Refined structure of bovine carboxypeptidase A at 1.25,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003Alexandra Kilshtain-Vardi The crystal structure of the bovine zinc metalloproteinase carboxypeptidase A (CPA) has been refined to 1.25,Å resolution based on room-temperature X-ray synchrotron data. The significantly improved structure of CPA at this resolution (anisotropic temperature factors, R factor = 10.4%, Rfree = 14.5%) allowed the modelling of conformational disorders of side chains, improved the description of the protein solvent network (375 water molecules) and provided a more accurate picture of the interactions between the active-site zinc and its ligands. The calculation of standard uncertainties in individual atom positions of the refined model of CPA allowed the deduction of the protonation state of some key residues in the active site and confirmed that Glu72 and Glu270 are negatively charged in the resting state of the enzyme at pH 7.5. These results were further validated by theoretical calculations that showed significant reduction of the pKa of these side chains relative to solution values. The distance between the zinc-bound solvent molecule and the metal ion is strongly suggestive of a neutral water molecule and not a hydroxide ion in the resting state of the enzyme. These findings could support both the general acid/general base mechanism, as well as the anhydride mechanism suggested for CPA. [source] Ultrahigh-resolution structure of high-potential iron,sulfur protein from Thermochromatium tepidumACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2002Lijun Liu Crystals of the high-potential iron,sulfur protein (HiPIP) from Thermochromatium tepidum diffract X-rays to 0.80,Å using synchrotron radiation at 100,K. The crystal structure of this HiPIP was refined at this ultrahigh resolution with anisotropic temperature factors for all atoms to conventional crystallographic R factors of 0.092 and 0.101 for Fo > 4,(Fo) and all reflections, respectively. The present structure provides a more precise picture than the previous 1.5,Å structure and allows location of the positions of most H atoms. The structure revealed a partly hydrophobic cavity near the main hydrophobic area and a much larger inter-cluster approach distance (23.454,Å, the c constant of the unit cell) in the crystal packing than other types of HiPIPs. The structural features involved in the electron-transfer reaction of HiPIP are discussed. [source] | ||||||||||