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SAD Data (sad + data)
Selected AbstractsDirect-method SAD phasing of proteins enhanced by the use of intrinsic bimodal phase distributions in the subsequent phase-improvement processACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2009Li-Jie Wu A modified SAD (single-wavelength anomalous diffraction) phasing algorithm has been introduced in the latest version of the program OASIS. In addition to direct-method phases and figures of merit, Hendrickson,Lattman coefficients that correspond to the original unresolved bimodal phase distributions are also output and used in subsequent phase-improvement procedures in combination with the improved phases. This provides the possibility of rebreaking the SAD phase ambiguity using the ever-improving phases resulting from the phase-improvement process. Tests using experimental SAD data from six known proteins showed that in all cases the new treatment produced significant improved results. [source] Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004Krzysztof Brzezinski The ,-1,6-fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus), composed of 325 amino acids with a molecular weight of 37,kDa, has been cloned, expressed and purified. Protein crystals suitable for X-ray diffraction were obtained under optimized crystallization conditions using ammonium dihydrogen phosphate as a precipitant. The crystals are hexagonal and belong to space group P6122 or P6522, with unit-cell parameters a = 125.5, c = 95.6,Å, and contain 56.8% solvent and a single protein molecule in the asymmetric unit. Native data were collected to 2.85,Å using synchrotron radiation and cryogenic conditions. The native crystals were soaked in a mother-liquor solution containing 2.5,mM [Ta6Br12]2+ cluster for derivatization and SAD data were collected to 3.4,Å at the tantalum LIII absorption peak. [source] Substructure solution with SHELXDACTA CRYSTALLOGRAPHICA SECTION D, Issue 10-2 2002Thomas R. Schneider Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0,3.5,Å, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package. [source] High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5,AMPACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001Pascal Retailleau Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS,adenylate product (TAM) complex to a resolution limit of 1.7,Å. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS combinations with native data. Hendrickson,Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9,Å structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25,Å and from the native model by 0.38,Å, but all have r.m.s. deviations of ,1.0,Å from the 2.9,Å model. Difference Fourier calculations between amplitudes from the 300,K experiment and the new amplitudes at 100,K using 1.7,Å model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria. [source] Crystallization and preliminary crystallographic analysis of nosiheptide-resistance methyltransferase from Streptomyces actuosus in complex with SAMACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Huirong Yang Nosiheptide-resistance methyltransferase (NSR) methylates 23S rRNA at the nucleotide adenosine 1067 in Escherichia coli and thus contributes to resistance against nosiheptide, a sulfur-containing peptide antibiotic. Here, the expression, purification and crystallization of NSR from Streptomyces actuosus are reported. Diffracting crystals were grown by the hanging-drop vapour-diffusion method in reservoir solution consisting of 0.35,M ammonium chloride, 24%(w/v) PEG 3350, 0.1,M MES pH 5.7 at 293,K. Native data have been collected from the apo enzyme and a SAM complex, as well as apo SeMet SAD data. The diffraction patterns of the apo form of NSR, of NSR complexed with SAM and of SeMet-labelled NSR crystals extended to 1.90, 1.95 and 2.25,Å resolution, respectively, using synchrotron radiation. All crystals belonged to space group P21, with approximate unit-cell parameters a = 64.6, b = 69.6, c = 64.9,Å, , = 117.8°. [source] | ||||||||||