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Synchrotron Data (synchrotron + data)
Selected AbstractsCharacterization and crystal structure of D -mannitol hemihydrateJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2004Cletus Nunes Abstract The objectives of this study were (i) to isolate and characterize mannitol hydrate, and (ii) to solve its crystal structure from high-resolution synchrotron X-ray powder diffraction data. Mannitol hydrate was prepared by freeze-drying aqueous mannitol solutions (5% w/v) under controlled conditions. X-ray powder diffractometry, differential scanning calorimetry, and thermogravimetric analyses indicated that mannitol exists as a hemihydrate (C6H14O6,·,0.5H2O). Synchrotron data were collected on the X3B1 beamline at the National Synchrotron Light Source. The simulated annealing program PSSP was used to solve the structure, which was subsequently refined by Rietveld analysis using the program package GSAS. The compound crystallizes in space group P1, with a,=,9.8963 Å, b,=,10.5424 Å, c,=,4.7860 Å, ,,=,102.589°, ,,=,86.092°, and ,,=,116.079°. The unit cell contains two dissimilar D -mannitol molecules and one water molecule, forming a hydrogen bonding pattern significantly different from that seen in the anhydrous polymorphs. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2800,2809, 2004 [source] Crystallization and preliminary X-ray diffraction studies of a fungal hydrolase from Ophiostoma novo-ulmiACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Michail N. Isupov Dutch elm disease fungus Ophiostoma novo-ulmi contains a hydrolase activity which catalyses the resolution of racemic ethyl naproxen to the corresponding acid. The recombinant enzyme has been crystallized by the vapour-diffusion method in two crystal forms. The crystals of the first form belong to space group P21212, with unit-cell parameters a = 115.9, b = 174.4, c = 62.1,Å. The enzyme also crystallizes in space group P21212, with unit-cell parameters a = 72.9, b = 212.7, c = 61.7,Å. Synchrotron data have been collected for both crystal forms to 2.6 and 2.3,Å, respectively. A molecular-replacement solution has been found using a remote starting model of a bacterial esterase (23% sequence identity) for both crystal forms. Multicrystal averaging has resulted in interpretable electron-density maps. [source] Disordered quasicrystals: diffuse scattering in decagonal Al,Ni,FeJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2004E. Weidner High-resolution synchrotron data of near-Bragg diffuse scattering from decagonal Al71.5Ni23.5Fe5 quasicrystals were recorded. A dominant phasonic origin is ruled out because of the absence of a significant G, dependence. An analysis solely in the frame of thermal diffuse scattering (TDS) theory (phonon scattering) showed a good match between experimental and calculated data in the quasiperiodic layers, but with an improbable ratio of elastic constants, c66/c11 = 4.0. In situ high-temperature measurements up to 1000,K revealed an increase of the intensity distribution perpendicular to the scattering vector G. Huang diffuse scattering (HDS) arising from quenched local defects has a general appearance that qualitatively reproduces the observed symmetry and anisotropy. An interpretation based on both TDS and HDS contributions is given. [source] X-Cell: a novel indexing algorithm for routine tasks and difficult casesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003Marcus A. Neumann X-Cell is a novel indexing algorithm that makes explicit use of systematic absences to search for possible indexing solutions from cells with low numbers of calculated reflections to cells with high numbers of reflections. Space groups with the same pattern of systematic absences are grouped together in powder extinction classes, and for a given peak number range an independent search is carried out in each powder extinction class. The method has the advantage that the correct cell is likely to be found before the rapid increase of possible solutions slows down the search significantly. A successive dichotomy approach is used to establish a complete list of all possible indexing solutions. The dichotomy procedure is combined with a search for the zero-point shift of the diffraction pattern, and impurity peaks can be dealt with by allowing for a user-defined portion of unindexed reflections. To rank indexing solutions with varying numbers of unindexed reflections, a new figure of merit is introduced that takes into account the highest level of agreement typically obtained for completely incorrect unit cells. The indexing of long and flat unit cells is facilitated by the possibility to search for rows or zones in reciprocal space first and then to use the lattice parameters of the dominant row or zone in the unit-cell search. The main advantages of X-Cell are robustness and completeness, as demonstrated by a validation study on a variety of compounds. The dominant phase of phase mixtures can be indexed in the presence of up to 50% of impurity peaks if high-quality synchrotron data are available. [source] Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycinACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010J. J. Holstein Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed. [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] Caged and clustered structures of endothelin inhibitor BQ123, cyclo(- d -Trp- d -Asp, -Pro- d -Val-Leu-),Na+, forming five and six coordination bonds between sodium ions and peptidesACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2001Mitsunobu Doi BQ123 is a cyclic pentapeptide and a potent endothelin-1 inhibitor. The crystal structure of the BQ123 sodium salt was determined as the first example of an endothelin inhibitor. Four independent molecules and many solvent molecules were found in the asymmetric unit; the total weight was about 3000,Da. The precise structure including the solvent molecules was determined using high-resolution data collected on a synchrotron source. Sodium ions formed unique structures with five and six coordination bonds and their forms were distinguished into three classes. An ion was sandwiched by two BQ123 molecules. This peptide,sodium (2:1) complex showed a cage-like structure and octahedral coordination was observed. Sodium ions also formed a cluster composed of hydrated water molecules and peptides. Two sodium ions were contained in this cluster, making five coordination bonds. Despite having the same coordination numbers, these ions were distinguishable by differences in the polyhedra. One was trigonal bipyramidal (having six planes) and the other was square pyramidal (having five planes). Both shapes were very similar to each other, although the synchrotron data clearly revealed slight geometrical differences. [source] Interaction of an echinomycin,DNA complex with manganese ionsACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Roland Pfoh The crystal structure of an echinomycin,d(ACGTACGT) duplex interacting with manganese(II) was solved by Mn-SAD using in-house data and refined to 1.1,Å resolution against synchrotron data. This complex crystallizes in a different space group compared with related complexes and shows a different mode of base pairing next to the bis-intercalation site, suggesting that the energy difference between Hoogsteen and Watson,Crick pairing is rather small. The binding of manganese to N7 of guanine is only possible because of DNA unwinding induced by the echinomycin, which might help to explain the mode of action of the drug. [source] Structure of pig heart citrate synthase at 1.78,Å resolutionACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Steven B. Larson Pig heart citrate synthase was crystallized from a small-molecule cocktail containing cystamine dihydrochloride, aspartame and benzamidine hydrochloride. The structure was refined to an R factor of 0.179 (Rfree = 0.222) using synchrotron data to a resolution of 1.78,Å. The model includes the full-length protein, a chloride ion, a sulfate ion, 305 water molecules and an unexpected moiety attached through a disulfide linkage to Cys184, which was modeled as a half-cystamine molecule generated by disulfide exchange with the cystamine in the small-molecule cocktail. [source] | ||||||||||