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Journal ArticleDOI

CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates

01 Dec 1995-Journal of Applied Crystallography (International Union of Crystallography)-Vol. 28, Iss: 6, pp 768-773
TL;DR: In this paper, a program for evaluating the solution scattering from macromolecules with known atomic structure is presented, which uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell.
Abstract: A program for evaluating the solution scattering from macromolecules with known atomic structure is presented. The program uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell. Given the atomic coordinates (e.g. from the Brookhaven Protein Data Bank) it can either predict the solution scattering curve or fit the experimental scattering curve using only two free parameters, the average displaced solvent volume per atomic group and the contrast of the hydration layer. The program runs on IBM PCs and on the major UNIX platforms.
Citations
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Journal ArticleDOI
TL;DR: Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.

2,105 citations


Cites methods from "CRYSOL : a program to evaluate X-ra..."

  • ...The envelopes of the ribosomal proteins were computed from their atomic coordinates in the Protein Data Bank (PDB, Bernstein et al., 1977) using the CRYSOL program ( Svergun et al., 1995 )....

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  • ...The envelopes of the ribosomal proteins were computed from their atomic coordinates in the Protein Data Bank (PDB, Bernstein et al., 1977) using the CRYSOL program (Svergun et al., 1995)....

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Journal ArticleDOI
TL;DR: The hand determination and refinement optimization procedure is applied to image pairs of the dihydrolipoyl acetyltransferase (E2) catalytic core of the pyruvate dehydrogenase complex from Bacillus stearothermophilus taken by low-dose electron cryomicroscopy.

1,959 citations

Journal ArticleDOI
TL;DR: The paper presents new developments and amendments to the ATSAS package (version 2.4) for processing and analysis of isotropic small-angle scattering data.
Abstract: New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.

1,634 citations


Cites methods from "CRYSOL : a program to evaluate X-ra..."

  • ...…intensities coming from different sources: (a) the theoretical scattering intensities from high-resolution PDB structures calculated by CRYSOL (Svergun et al., 1995), (b) the experimental scattering curves and (c) the regularized (and desmeared if necessary) scattering curves obtained by GNOM…...

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  • ...Originally (Petoukhov et al., 2007), the interfaces to the ab initio programs DAMMIN (Svergun, 1999) and GASBOR (Svergun et al., 2001) and atomic structure-based programs CRYSOL (Svergun et al., 1995) and SASREF (Petoukhov & Svergun, 2005) were provided....

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  • ...The programs CRYSOL (Svergun et al., 1995) for X-rays and CRYSON (Svergun et al., 1998) for neutrons evaluate the solution scattering from macromolecules with known atomic structure and fit a predicted curve IcalcðsÞ to experimental scattering data IexpðsÞ by minimizing the discrepancy (Feigin &…...

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  • ...…taken from the Protein Data Bank (PDB; Bernstein et al., 1977) (of these, 34 and 11 proteins were solved by X-ray and electron crystallography, respectively, and eight were obtained by NMR), and their theoretical scattering intensities were computed using the program CRYSOL (Svergun et al., 1995)....

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Journal ArticleDOI
07 May 2009-Nature
TL;DR: The DNA origami method is extended into three dimensions by creating an addressable DNA box that can be opened in the presence of externally supplied DNA ‘keys’, and controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications.
Abstract: By exploiting the unique structural motifs and self-recognition properties of DNA, it is possible to generate self-assembled DNA nanostructures of specific shapes. Here, a previously described DNA 'origami' method has been extended into three dimensions to create an addressable DNA box on the nanometre scale that can be opened by an externally supplied DNA key'.

1,458 citations

Journal ArticleDOI
TL;DR: The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins.

1,363 citations


Cites methods from "CRYSOL : a program to evaluate X-ra..."

  • ...puted using the program CRYSOL (Svergun et al., 1995) assuming the bound solvent to be 10% denser than the bulk (drb 5 30 e/nm (3); Svergun et al....

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  • ...© 2001 by the Biophysical Society 0006-3495/01/06/2946/08 $2.00 puted using the program CRYSOL (Svergun et al., 1995) assuming the bound solvent to be 10% denser than the bulk (drb 5 30 e/nm 3; Svergun et al., 1995, 1998)....

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  • ...The scattering pattern computed using CRYSOL with coordinates from the ligand-bound form of HSA yielded a better fit to the experimental data compared with the ligandfree form....

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References
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01 Jan 1960
TL;DR: In this paper, the angular momentum, one of the most fundamental quantities in all of quantum mechanics, is introduced and a concise introduction to its application in atomic, molecular, and nuclear physics is provided.
Abstract: This book offers a concise introduction to the angular momentum, one of the most fundamental quantities in all of quantum mechanics. Beginning with the quantization of angular momentum, spin angular momentum, and the orbital angular momentum, the author goes on to discuss the Clebsch-Gordan coefficients for a two-component system. After developing the necessary mathematics, specifically spherical tensors and tensor operators, the author then investigates the 3-j, 6-j, and 9-j symbols. Throughout, the author provides practical applications to atomic, molecular, and nuclear physics. These include partial-wave expansions, the emission and absorption of particles, the proton and electron quadrupole moment, matrix element calculation in practice, and the properties of the symmetrical top molecule.

5,050 citations

Book
21 Sep 1957
TL;DR: In this article, the angular momentum, one of the most fundamental quantities in all of quantum mechanics, is introduced and a concise introduction to its application in atomic, molecular, and nuclear physics is provided.
Abstract: This book offers a concise introduction to the angular momentum, one of the most fundamental quantities in all of quantum mechanics. Beginning with the quantization of angular momentum, spin angular momentum, and the orbital angular momentum, the author goes on to discuss the Clebsch-Gordan coefficients for a two-component system. After developing the necessary mathematics, specifically spherical tensors and tensor operators, the author then investigates the 3-j, 6-j, and 9-j symbols. Throughout, the author provides practical applications to atomic, molecular, and nuclear physics. These include partial-wave expansions, the emission and absorption of particles, the proton and electron quadrupole moment, matrix element calculation in practice, and the properties of the symmetrical top molecule.

4,377 citations