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Patterson Map (patterson + map)
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] The combined use of Patterson and Monte Carlo methods for the decomposition of a powder diffraction patternJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2006Angela Altomare The success of ab initio crystal structure solution by powder diffraction data is strictly related to the quality of the integrated intensity estimates. A new method that is able to improve the pattern decomposition step has been developed. It combines the inversion of a suitably modified Patterson map with the use of the Hamming codes [13,10] and [40,36] in order to explore more decomposition trials. The new approach has been introduced in EXPO2005, an updated version of EXPO2004, and successfully applied to a set of known organic and inorganic structures. [source] Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1CACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Yingssu Tsai Lattice-translocation or crystal order,disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two layers of cyclic protein hexamers. The first layer is fully ordered (i.e. has one fixed position), while the second layer randomly takes one of three alternative positions whose displacements are related to each other by threefold symmetry. Remarkably, the highest symmetry present in the crystal is P3, yet the intensity data (and the Patterson map) obey 6/m instead of symmetry; the intensities exceed the symmetry expected from combining the crystal space group with an inversion center. The origin of this rare phenomenon, known as symmetry enhancement, is discussed and shown to be possible even for a perfectly ordered crystal. The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions. [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] Purification, crystallization and preliminary X-ray diffraction of a proteolytic fragment of PDK1 containing the pleckstrin homology domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004David Komander 3-Phosphoinositide-dependent protein kinase-1 (PDK1) is a Ser/Thr kinase with an essential role in insulin and growth-factor signalling. PDK1 activity towards protein kinase B (PKB) is partially regulated by its pleckstrin homology (PH) domain, which preferentially binds to 3-phosphoinositides. However, the precise molecular mechanism of this regulation is not well understood. Here, the cloning, purification and crystallization of a 150-amino-acid C-terminal region of PDK1 containing the PH domain is reported. A crystal of the PDK1 PH domain grown in the presence of inositol 1,3,4,5-tetrakisphosphate and derivatized with AuCN diffracted to 1.5,Å at a synchrotron source. Diffraction data collected near the Au edge resulted in an anomalous Patterson map with a 30, peak. [source] Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana pereziACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003Eva Valencia Different crystal forms diffracting to high resolution have been obtained for two NADP(H)-dependent alcohol dehydrogenases, members of the medium-chain dehydrogenase/reductase superfamily: ScADHVI from Saccharomyces cerevisiae and ADH8 from Rana perezi. ScADHVI is a broad-specificity enzyme, with a sequence identity lower than 25% with respect to all other ADHs of known structure. The best crystals of ScADHVI diffracted beyond 2.8,Å resolution and belonged to the trigonal space group P3121 (or to its enantiomorph P3221), with unit-cell parameters a = b = 102.2, c = 149.7,Å, , = 120°. These crystals were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Packing considerations together with the self-rotation function and the native Patterson map seem to indicate the presence of only one subunit per asymmetric unit, with a volume solvent content of about 80%. ADH8 from R. perezi is the only NADP(H)-dependent ADH from vertebrates characterized to date. Crystals of ADH8 obtained both in the absence and in the presence of NADP+ using polyethylene glycol and lithium sulfate as precipitants diffracted to 2.2 and 1.8,Å, respectively, using synchrotron radiation. These crystals were isomorphous, space group C2, with approximate unit-cell parameters a = 122, b = 79, c = 91,Å, , = 113° and contain one dimer per asymmetric unit, with a volume solvent content of about 50%. [source] Crystallization and preliminary X-ray diffraction studies of a novel alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernixACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2003Jodie E. Guy A novel alcohol dehydrogenase enzyme has been cloned from the hyperthermophilic archaeon Aeropyrum pernix and overexpressed in Escherichia coli. This zinc-containing enzyme has been crystallized by the sitting-drop vapour-diffusion method using PEG 600 as precipitant. The crystals diffract to 1.5,Å resolution and belong to the orthorhombic space group P21212, with unit-cell parameters a = 100.7, b = 103.2, c = 67.5,Å. The asymmetric unit contains two enzyme monomers. Two synchrotron data sets have been collected: one at a wavelength near the absorption edge of zinc and one at a remote wavelength. Three strong zinc-ion positions were visible in the anomalous Patterson map. Two additional weaker zinc ions have been identified by anomalous Fourier synthesis. [source] Use of Cr K, radiation to enhance the signal from anomalous scatterers including sulfurJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-2 2000Witek Kwiatkowski The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the Cr K, radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the Cu K, and Cr K, data were similar but better than that for Au L,. This result was in spite of the fourfold higher flux from the Cu anode versus the Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the Cr K, data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the Au L, data. The ability to enhance the S-derived anomalous signal using Cr K, radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the Cr K, data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method. [source] Application of general formulas for the correction of a lattice-translocation defect in crystals of a lentiviral integrase in complex with LEDGFACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Stephen Hare The symmetry inherent to many biological macromolecular assemblies has been implicated in a range of crystal pathologies, including lattice-translocation defects (LTDs). Crystals suffering from classic LTDs contain two lattices that are shifted with respect to each other but nonetheless remain within the length of coherent interference. LTD introduces an undesirable intensity modulation into diffraction data, resulting in scrambled or partially scrambled electron densities. In this report, LTD theory is extended and a new general method for determining defect fractions is developed based on the heights of the non-origin peaks observed in native Patterson maps. The application of this method to crystals of lentiviral integrase in complex with its cofactor, where the observed translocation vector does not equal a small integral fraction of a unit-cell edge, is reported and its general application to all classic LTD cases is predicted. [source] Crystallization of FLINC4, an intramolecular LMO4,ldb1 complexACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003Janet E. Deane LMO4 is the most recently discovered member of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO4 is comprised primarily of two tandemly repeated LIM domains and interacts with the ubiquitous nuclear adaptor protein ldb1. This interaction is mediated via the LIM domains of LMO4 and the LIM-interaction domain (LID) of ldb1. An intramolecular complex, termed FLINC4, consisting of the two LIM domains from LMO4 linked to the LID domain of ldb1 via a flexible linker has been engineered, purified and crystallized. The trigonal crystals, which belong to space group P312 with unit-cell parameters a = 61.3, c = 93.2,Å, diffract to 1.3,Å resolution and contain one molecule of FLINC4 per asymmetric unit. Native and multiple-wavelength anomalous dispersion (MAD) data collected at the Zn X-ray absorption edge have been recorded to 1.3 and 1.7,Å resolution, respectively. Anomalous Patterson maps calculated with data collected at the peak wavelength show strong peaks sufficient to determine the positions of four Zn atoms per asymmetric unit. [source] Phasing power at the K absorption edge of organic arsenicACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2003Pascal Retailleau Single/multiple-wavelength anomalous dispersion (SAD/MAD) experiments were performed on a crystal of an organic arsenic derivative of hen egg-white lysozyme. A para -arsanilate compound used as a crystallizing reagent was incorporated into the ordered solvent region of the lysozyme molecule. Diffraction data were collected to high resolution (,2.0,Å) at three wavelengths around the K edge (1.04,Å) of arsenic at beamline BM30A, ESRF synchrotron. Anomalous Patterson maps clearly showed the main arsanilate site to be between three symmetry-related lysozyme molecules, at a location previously occupied by a para -toluenesulfonate anion. MAD phases at 2,Å derived using the program SHARP led to an electron-density map of sufficient quality to start manual building of the protein model. Amplitudes from a second crystal measured to a resolution of 1.8,Å at the peak wavelength revealed two additional heavy-atom sites, which reinforced the anomalous subset model and therefore dramatically improved the phasing power of the arsenic derivative. The subsequent solvent-flattened map was of such high accuracy that the program ARP/wARP was able to build a nearly complete model automatically. This work emphasizes the great potential of arsenic for de novo structure determination using anomalous dispersion methods. [source] Crystallization and preliminary X-ray analysis of a C-terminal fragment of FlgJ, a putative flagellar rod cap protein from SalmonellaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2009Yuki Kikuchi The formation of the bacterial flagellar axial structure, including the filament, the hook and the rod, requires the attachment of a cap complex to the distal end of the growing structure. Because the rod penetrates the peptidoglycan (PG) layer, the rod cap complex is thought to have PG-hydrolyzing activity. FlgJ is a putative rod cap protein whose C-terminal region shows sequence similarity to known muramidases. In this study, FlgJ120,316, a C-terminal fragment of FlgJ which contains the muramidase region, was overproduced, purified and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion technique using PEG 3350 as a crystallizing agent and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 38.8, b = 43.9, c = 108.5,Å. Anomalous difference Patterson maps calculated from the diffraction data set of a selenomethionine-labelled crystal showed significant peaks in the Harker sections, indicating that the data were suitable for structure determination. [source] | ||||||||||