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Molecular Envelope (molecular + envelope)
Selected AbstractsCombining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sitesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2009Xinguo Hong Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the program GASBOR at 5,Å resolution (qmax = 1.25,Å,1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8,Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2, level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax = 0.25,Å,1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination of FSEARCH and WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement. [source] Ultralow-resolution ab initio phasing of filamentous proteins: crystals from a six-Ig fragment of titin as a case studyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2008Alexandre Urzhumtsev Low-resolution diffraction data (resolution below 12,Å) from crystals of a filamentous six-Ig fragment of titin, I65,I70, were used in ab initio phasing with the aim of calculating its lattice packing and molecular envelope. Filamentous molecules, characterized by marked anisometry and idiosyncratic crystal lattices, have not been addressed before using this methodology. In this study, low-resolution phasing (19,122,Å) successfully identified the region of the unit cell occupied by the molecule. Phase extension to a higher resolution (12,Å) yielded regions of high density that corresponded either to the positions of individual Ig domains or to zones of dense intermolecular contacts, hindering the identification of individual domains and the interpretation of electron-density maps in terms of a molecular model. This problem resulted from the acutely uneven packing of the molecules in the crystal and it was further accentuated by the presence of partially disordered regions in the molecule. Addition of low-resolution reflections with phases computed ab initio to those obtained experimentally using MIRAS improved the initial electron-density maps of the atomic model, demonstrating the generic utility of low-resolution phases for the structure-elucidation process, even when individual molecules cannot be resolved in the lattice. [source] Determination of molecular envelopes from solvent contrast variation dataACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Victor Lo An algorithm is described for determining macromolecular envelopes from crystal diffraction amplitudes measured from a solvent contrast variation series. The method uses solvent contrast variation data that have been preprocessed to represent the structure-factor amplitudes of the envelope. The amplitudes are phased using an iterative projection algorithm that incorporates connectivity and compactness constraints on the envelope. The algorithm is tested by simulation on two protein envelopes and shown to be effective even in the absence of the very low resolution data, which are difficult to access experimentally. [source] An evolutionary computational approach to the phase problem in macromolecular X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2001Gordon Webster The ab initio computation of the molecular envelopes of two proteins exclusively from their corresponding diffraction amplitudes demonstrates that an efficient and inherently parallel evolutionary search algorithm can assist in the direct phasing of macromolecules for which almost no a priori structural information is available. The applicability of this evolutionary computational approach is general and should not be limited to the examples described nor to extremes of data resolution, symmetry or structural size. [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] | ||||||||||