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Title: Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilarmore » diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less
Authors:
 [1] ;  [2] ; ;  [3] ;  [4] ;  [2] ;  [2] ;  [5] ;  [6] ;  [7] ;  [1]
  1. University of California San Francisco, San Francisco, CA 94158 (United States)
  2. Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)
  3. Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)
  4. Australian National University, Canberra, ACT 2601 (Australia)
  5. (United States)
  6. Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France)
  7. (France)
Publication Date:
OSTI Identifier:
22389077
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal Issue: Pt 8; Other Information: PMCID: PMC4528799; PMID: 26249347; PUBLISHER-ID: rr5095; OAI: oai:pubmedcentral.nih.gov:4528799; Copyright (c) Van Benschoten et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ACCURACY; ATOMIC DISPLACEMENTS; ATOMS; AUGMENTATION; BRAGG REFLECTION; CORRELATIONS; CRYSTALLOGRAPHY; DENSITY; DIFFUSE SCATTERING; DISTRIBUTION; ELECTRON DENSITY; ELECTRONS; EXPERIMENTAL DATA; POTENTIALS