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X-ray Scattering Data (x-ray + scattering_data)
Selected AbstractsLow-resolution structure of immunoglobulins IgG1, IgM and rheumatoid factor IgM-RF from solution X-ray scattering dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2003Vladimir V. Volkov Low-resolution structures of immunoglobulins IgG, IgM and rheumatoid factor IgM-RF in solution were analyzed using synchrotron radiation small-angle X-ray scattering and the macromolecular shapes were restored ab initio from the scattering data. The shape of IgG agrees well with the distorted Y-type crystallographic model but has a swollen appearance reflecting flexibility of the molecule in solution. The structures of pentameric IgM and IgM-RF were reconstructed assuming a five-fold symmetry. The IgM displays a flat star-like shape with observable F(ab)2 regions. The overall shape of the IgM-RF is similar to that of the IgM but with distinctly asymmetric F(ab)2 regions. This result agrees with the earlier observed functional dissimilarity of the Fab fragments in the rheumatoid factor and points to their structural dissimilarity. [source] Modelling of small-angle X-ray scattering data using Hermite polynomialsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2001A. K. Swain A new algorithm, called the term-selection algorithm (TSA), is derived to treat small-angle X-ray scattering (SAXS) data by fitting models to the scattering intensity using weighted Hermite polynomials. This algorithm exploits the orthogonal property of the Hermite polynomials and introduces an error-reduction ratio test to select the correct model terms or to determine which polynomials are to be included in the model and to estimate the associated unknown coefficients. With no a priori information about particle sizes, it is possible to evaluate the real-space distribution function as well as three- and one-dimensional correlation functions directly from the models fitted to raw experimental data. The success of this algorithm depends on the choice of a scale factor and the accuracy of orthogonality of the Hermite polynomials over a finite range of SAXS data. An algorithm to select a weighted orthogonal term is therefore derived to overcome the disadvantages of the TSA. This algorithm combines the properties and advantages of both weighted and orthogonal least-squares algorithms and is numerically more robust for the estimation of the parameters of the Hermite polynomial models. The weighting feature of the algorithm provides an additional degree of freedom to control the effects of noise and the orthogonal feature enables the reorthogonalization of the Hermite polynomials with respect to the weighting matrix. This considerably reduces the error in orthogonality of the Hermite polynomials. The performance of the algorithm has been demonstrated considering both simulated data and experimental data from SAXS measurements of dewaxed cotton fibre at different temperatures. [source] Advanced solution scattering data analysis methods and their applicationsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2000D. I. Svergun A method for ab initio low-resolution shape and internal structure retrieval from contrast variation solution scattering data is described. The method uses a multiphase model of a particle build from densely packed dummy atoms and employs simulated annealing to find a compact interconnected configuration of phases that fits the available experimental data. In the particular case of a single phase particle (shape determination) the method is compared to another ab initio method using low resolution envelope functions. Examples of the shape determination of several proteins from experimental X-ray scattering data are presented. [source] High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrityJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2003Robert F. Fischetti Wide-angle X-ray scattering patterns from proteins in solution contain information relevant to the determination of protein fold. At relevant scattering angles, however, these data are weak, and the degree to which they might be used to categorize the fold of a protein is unknown. Preliminary work has been performed at the BioCAT insertion-device beamline at the Advanced Photon Source which demonstrates that one can collect X-ray scattering data from proteins in solution to spacings of at least 2.2,Å (q = 2.8,Å,1). These data are sensitive to protein conformational states, and are in good agreement with the scattering predicted by the program CRYSOL using the known three-dimensional atomic coordinates of the protein. An important issue in the exploitation of this technique as a tool for structural genomics is the extent to which the high intensity of X-rays available at third-generation synchrotron sources chemically or structurally damage proteins. Various data-collection protocols have been investigated demonstrating conditions under which structural degradation of even sensitive proteins can be minimized, making this technique a viable tool for protein fold categorization, the study of protein folding, unfolding, protein,ligand interactions and domain movement. [source] Analysis of time-resolved X-ray scattering data from solution-state systemsACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010Kristoffer Haldrup As ultrafast time-resolved studies of liquid systems with the laser pump/X-ray scattering probe method have come of age over the past decade, several groups have developed methods for the analysis of such X-ray scattering data. The present article describes a method developed primarily with a focus on determining structural parameters in the excited states of medium-sized molecules (~30 atoms) in solution. The general methodology is set in a maximum-likelihood framework and is introduced through the analysis of the photoactive platinum compound PtPOP, in particular the structure of its lowest triplet excited state (3A2u). Emphasis is put on structure determination in terms of model comparisons and on the information content of difference scattering signals as well as the related experimental variables. Several suggestions for improving the accuracy of these types of measurements are presented. [source] Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scatteringPROTEIN SCIENCE, Issue 4 2009Pau Bernadó Abstract Signal transducer and activator of transcription (STAT) proteins play a crucial role in the activation of gene transcription in response to extracellular stimuli. The regulation and activity of these proteins require a complex rearrangement of the domains. According to the established models, based on crystallographic data, STATs convert from a basal antiparallel inactive dimer into a parallel active one following phosphorylation. The simultaneous analysis of small-angle X-ray scattering data measured at different concentrations of unphosphorylated human STAT5a core domain unambiguously identifies the simultaneous presence of a monomer and a dimer. The dimer is the minor species but could be structurally characterized by SAXS in the presence of the monomer using appropriate computational tools and shown to correspond to the antiparallel assembly. The equilibrium is governed by a moderate dissociation constant of Kd , 90 ,M. Integration of these results with previous knowledge of the N-terminal domain structure and dissociation constants allows the modeling of the full-length protein. A complex network of intermolecular interactions of low or medium affinity is suggested. These contacts can be eventually formed or broken to trigger the dramatic modifications in the dimeric arrangement needed for STAT regulation and activity. [source] Single-crystal diffuse scattering studies on polymorphs of molecular crystals.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009The drug benzocaine (ethyl 4-aminobenzoate), commonly used as a local anaesthetic, is a bimorphic solid at room temperature. Form (I) is monoclinic P21/c, while the metastable form (II) is orthorhombic P212121. Three-dimensional diffuse X-ray scattering data have been collected for the two forms on the 11-ID-B beamline at the Advanced Photon Source (APS). Both forms show strong and highly structured diffuse scattering. The data have been interpreted and analysed using Monte Carlo (MC) modelling on the basis that the scattering is purely thermal in origin and indicates the presence of highly correlated molecular motions. In both forms (I) and (II) broad diffuse streaks are observed in the 0kl section which indicate strong longitudinal displacement correlations between molecules in the ,031, directions, extending over distances of up to 50,Å. Streaks extending between Bragg peaks in the hk0 section normal to [100] correspond to correlated motions of chains of molecules extending along a that are linked by N,H...O=C hydrogen bonds and which occur together as coplanar ribbon pairs. The main difference between the two forms is in the dynamical behaviour of the ribbon pairs and in particular how they are able to slide relative to each other. While for form (I) a model involving harmonic springs is able to describe the motion satisfactorily, as simple excursions away from the average structure, there is evidence in form (II) of anharmonic effects that are precursors of a phase transition to a new low-temperature phase, form (III), that was subsequently found. [source] | ||||||||||