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Symmetry Operators (symmetry + operators)
Selected AbstractsTeaching crystallography to undergraduate physical chemistry studentsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5-2 2010Virginia B. Pett Teaching goals, laboratory experiments and homework assignments are described for teaching crystallography as part of two undergraduate physical chemistry courses. A two-week teaching module is suggested for introductory physical chemistry, including six to eight classroom sessions, several laboratory experiences and a 3,h computer-based session, to acquaint undergraduate physical chemistry students with crystals, diffraction patterns, the mathematics of structure determination by X-ray diffraction, data collection, structure solution and the chemical insights available from crystal structure information. Student projects and laboratory work for three to four weeks of an advanced physical chemistry course are presented. Topics such as symmetry operators, space groups, systematic extinctions, methods of solving the phase problem, the Patterson map, anomalous scattering, synchrotron radiation, crystallographic refinement, hydrogen bonding and neutron diffraction all lead to the goal of understanding and evaluating a crystallographic journal article. Many of the ideas presented here could also be adapted for inorganic chemistry courses. [source] Ethyl[tris(3- tert -butyl-5-methylpyrazol-1-yl)hydridoborato]zinc(II)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010Mukesh Kumar The X-ray crystal structure of the title compound, [Zn(C2H5)(C24H40BN6)], or TptBu,MeZnEt [TptBu,Me is tris(3- tert -butyl-5-methylpyrazolyl)hydridoborate], reveals a distorted tetrahedral geometry around the Zn atom. The Zn center is coordinated by three N atoms of the borate ligand and by one C atom of the ethyl group. The present structure and other tetrahedral Tp zinc alkyl complexes are compared with similar Ttz ligands (Ttz is 1,2,4-triazolylborate), but no major differences in the structures are noted, and it can be assumed that variation of the substitution pattern of Tp or Ttz ligands has little or no influence on the geometry of alkylzinc complexes. Refinement of the structure is complicated by a combination of metric pseudosymmetry and twinning. The metrics of the structure could also be represented in a double-volume C -centered orthorhombic unit cell, and the structure is twinned by one of the orthorhombic symmetry operators not present in the actual structure. The twinning lies on the borderline between pseudomerohedral and nonmerohedral. The data were refined as being nonmerohedrally twinned, pseudomerohedrally twinned and untwinned. None of the approaches yielded results that were unambiguously better than any of the others: the best fit between structural model and data was observed using the nonmerohedral approach which also yielded the best structure quality indicators, but the data set is less than 80% complete due to rejected data. The pseudomerohedral and the untwinned structures are complete, but relatively large residual electron densities that are not close to the metal center are found with values up to three times higher than in the nonmerohedral approach. [source] A description of the structural determination procedures of a gap junction channel at 3.5,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009Michihiro Suga Intercellular signalling is an essential characteristic of multicellular organisms. Gap junctions, which consist of arrays of intercellular channels, permit the exchange of ions and small molecules between adjacent cells. Here, the structural determination of a gap junction channel composed of connexin 26 (Cx26) at 3.5,Å resolution is described. During each step of the purification process, the protein was examined using electron microscopy and/or dynamic light scattering. Dehydration of the crystals improved the resolution limits. Phase refinement using multi-crystal averaging in conjunction with noncrystallographic symmetry averaging based on strictly determined noncrystallographic symmetry operators resulted in an electron-density map for model building. The amino-acid sequence of a protomer structure consisting of the amino-terminal helix, four transmembrane helices and two extracellular loops was assigned to the electron-density map. The amino-acid assignment was confirmed using six selenomethionine (SeMet) sites in the difference Fourier map of the SeMet derivative and three intramolecular disulfide bonds in the anomalous difference Fourier map of the native crystal. [source] Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Megan Guelker The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0,Å resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (,h, ,k, l), was required to converge to reasonable R -factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition. [source] | ||||||||||