Measuring and modeling diffuse scattering in protein X-ray crystallography
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Nicholas K Sauter | Lin Liu | Ana Gonzalez | Michael E Wall | James S Fraser | Aaron S Brewster | Andrew H. Van Benschoten | Andrew H Van Benschoten | M. Wall | J. Fraser | N. Sauter | A. Brewster | Ana González | Lin Liu
[1] Nicholas K. Sauter,et al. dxtbx: the diffraction experiment toolbox , 2013, Journal of applied crystallography.
[2] N Go,et al. Dynamic structure of human lysozyme derived from X-ray crystallography: normal mode refinement. , 1994, Biophysical chemistry.
[3] André Guinier,et al. X-ray Crystallography. (Book Reviews: X-Ray Diffraction in Crystals, Imperfect Crystals, and Amorphous Bodies) , 1963 .
[4] Jianpeng Ma,et al. Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit , 2009, Acta crystallographica. Section D, Biological crystallography.
[5] Jeremy C Smith,et al. Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. , 2005, Physical review letters.
[6] Nicholas K. Sauter,et al. The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework , 2002 .
[7] J. Clarage,et al. Liquid-like movements in crystalline insulin , 1988, Nature.
[8] Mark A. Wilson,et al. Visualizing networks of mobility in proteins , 2013, Nature Methods.
[9] Jeremy C. Smith,et al. Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. , 2005, Biophysical journal.
[10] Jeremy C. Smith,et al. Protein dynamics from X‐ray crystallography: Anisotropic, global motion in diffuse scattering patterns , 2006, Proteins.
[11] K. N. Trueblood,et al. On the rigid-body motion of molecules in crystals , 1968 .
[12] N Go,et al. Collective motions in proteins investigated by X‐ray diffuse scattering , 1994, Proteins.
[13] Michael E Wall. Methods and software for diffuse X-ray scattering from protein crystals. , 2009, Methods in molecular biology.
[14] Henry van den Bedem,et al. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit , 2015, bioRxiv.
[15] P. Zwart,et al. Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.
[16] P. Moore,et al. On the relationship between diffraction patterns and motions in macromolecular crystals. , 2009, Structure.
[17] Reginald W. James,et al. The Optical principles of the diffraction of X-rays , 1948 .
[18] Zbigniew Dauter,et al. On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin. , 2013, Acta crystallographica. Section D, Biological crystallography.
[19] Graeme Winter,et al. Decision making in xia2 , 2013, Acta crystallographica. Section D, Biological crystallography.
[20] Sol M. Gruner. X-ray imaging detectors , 2012 .
[21] Nathaniel Echols,et al. Accessing protein conformational ensembles using room-temperature X-ray crystallography , 2011, Proceedings of the National Academy of Sciences.
[22] I. Bahar,et al. Global dynamics of proteins: bridging between structure and function. , 2010, Annual review of biophysics.
[23] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[24] Jeremy C. Smith,et al. X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation. , 1998, Journal of molecular biology.
[25] Randy J. Read,et al. Phaser crystallographic software , 2007, Journal of applied crystallography.
[26] Jeremy C. Smith,et al. Correlated intramolecular motions and diffuse x–ray scattering in lysozyme , 1994, Nature Structural Biology.
[27] David S Cerutti,et al. Peptide crystal simulations reveal hidden dynamics. , 2013, Journal of the American Chemical Society.
[28] S M Gruner,et al. Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[29] Jay Painter,et al. Electronic Reprint Biological Crystallography a Molecular Viewer for the Analysis of Tls Rigid-body Motion in Macromolecules Biological Crystallography a Molecular Viewer for the Analysis of Tls Rigid-body Motion in Macromolecules , 2022 .
[30] G. Phillips,et al. Diffuse x-ray scattering from tropomyosin crystals. , 1992, Biophysical journal.
[31] Pawel A. Janowski,et al. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice , 2016, Protein science : a publication of the Protein Society.
[32] R M Sweet,et al. Correlations of atomic movements in lysozyme crystals , 1992, Proteins.
[33] Axel T. Brunger,et al. Thermal Motion and Conformational Disorder in Protein Crystal Structures: Comparison of Multi‐Conformer and Time‐Averaging Models , 1994 .
[34] A. Kolinski,et al. Elastic network normal modes provide a basis for protein structure refinement. , 2012, The Journal of chemical physics.
[35] Jianpeng Ma,et al. A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography , 2008, Proceedings of the National Academy of Sciences.
[36] G. Phillips,et al. Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.
[37] Ankur Dhanik,et al. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers. , 2009, Acta crystallographica. Section D, Biological crystallography.
[38] Michael E. Wall,et al. Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles , 2015 .
[39] M E Wall,et al. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. , 1997, Structure.
[40] Franci Merzel,et al. Lattice dynamics of a protein crystal. , 2007, Physical review letters.
[41] John Kuriyan,et al. Exploration of disorder in protein structures by X‐ray restrained molecular dynamics , 1991, Proteins.
[42] Alexandre Urzhumtsev,et al. From deep TLS validation to ensembles of atomic models built from elemental motions , 2015, bioRxiv.
[43] H. N. Chapman,et al. Imaging Atomic Structure and Dynamics with Ultrafast X-ray Scattering , 2007, Science.
[44] I. Taylor,et al. Diffuse scattering resulting from macromolecular frustration. , 2011, Acta crystallographica. Section B, Structural science.
[45] Paul D Adams,et al. Modelling dynamics in protein crystal structures by ensemble refinement , 2012, eLife.
[46] Andrew L. Goodwin,et al. The crystallography of correlated disorder , 2015, Nature.
[47] J B Clarage,et al. Analysis of diffuse scattering from yeast initiator tRNA crystals. , 1994, Acta crystallographica. Section D, Biological crystallography.
[48] Mark A. Wilson,et al. Intrinsic motions along an enzymatic reaction trajectory , 2007, Nature.
[49] G. Phillips,et al. Motions of tropomyosin. Crystal as metaphor. , 1980, Biophysical journal.
[50] H. V. D. Bedem,et al. Automated identification of functional dynamic contact networks from X-ray crystallography , 2013 .
[51] Ivet Bahar,et al. ProDy: Protein Dynamics Inferred from Theory and Experiments , 2011, Bioinform..
[52] G. Phillips,et al. Analysis of diffuse scattering and relation to molecular motion. , 1997, Methods in enzymology.
[53] Peixiang Ma,et al. Observing the overall rocking motion of a protein in a crystal , 2015, Nature Communications.
[54] B M Pettitt,et al. A sampling problem in molecular dynamics simulations of macromolecules. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[55] Jianpeng Ma,et al. Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution , 2007, Proceedings of the National Academy of Sciences.
[56] J. Fraser,et al. Integrative, dynamic structural biology at atomic resolution—it's about time , 2015, Nature Methods.
[57] D. Kern,et al. Hidden alternate structures of proline isomerase essential for catalysis , 2010 .
[58] George N Phillips,et al. Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering. , 2010, Biophysical journal.
[59] P. Moore,et al. Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals. , 2015, Acta crystallographica. Section D, Biological crystallography.
[60] Nicholas K Sauter,et al. Diffuse X-ray scattering to model protein motions. , 2014, Structure.
[61] Guang Song,et al. How well can we understand large-scale protein motions using normal modes of elastic network models? , 2007, Biophysical journal.
[62] Randy J. Read,et al. Acta Crystallographica Section D Biological , 2003 .
[63] J. Pérez,et al. Molecular rigid-body displacements in a tetragonal lysozyme crystal confirmed by X-ray diffuse scattering. , 1996, Acta crystallographica. Section D, Biological crystallography.
[64] J. Doucet,et al. Molecular dynamics studied by analysis of the X-ray diffuse scattering from lysozyme crystals , 1987, Nature.
[65] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[66] Axel T Brunger,et al. Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. , 2004, Journal of molecular biology.
[67] Bojan Zagrovic,et al. Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures , 2011, Journal of molecular biology.
[68] David S. Moss,et al. Protein dynamics: use of computer graphics and protein crystal diffuse scattering recorded with synchrotron X-radiation , 1986 .
[69] Andrew H. Van Benschoten,et al. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering , 2014, Proceedings of the National Academy of Sciences.
[70] T. Welberry,et al. Diffuse X-ray Scattering and Models of Disorder , 2004 .
[71] Jay Painter,et al. Electronic Reprint Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion , 2005 .