Recent developments in phasing and structure refinement for macromolecular crystallography.

Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental diffraction data and prior chemical knowledge. Recent advances in phasing and model refinement and validation algorithms make it possible to arrive at better electron density maps and more accurate models.

[1]  G. Bricogne,et al.  [27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. , 1997, Methods in enzymology.

[2]  B. C. Wang Resolution of phase ambiguity in macromolecular crystallography. , 1985, Methods in enzymology.

[3]  M. Vijayan,et al.  Isomorphous replacement and anomalous scattering , 2006 .

[4]  G. Bricogne Geometric sources of redundancy in intensity data and their use for phase determination , 1974 .

[5]  G N Murshudov,et al.  Incorporation of prior phase information strengthens maximum-likelihood structure refinement. , 1998, Acta crystallographica. Section D, Biological crystallography.

[6]  Jean-Michel Claverie,et al.  CaspR: a web server for automated molecular replacement using homology modelling , 2004, Nucleic Acids Res..

[7]  D. Baker,et al.  RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation , 2008, Protein science : a publication of the Protein Society.

[8]  H. Hauptman,et al.  Optimizing statistical Shake-and-Bake for Se-atom substructure determination. , 2005, Acta crystallographica. Section D, Biological crystallography.

[9]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Likelihood-enhanced Fast Rotation Functions Biological Crystallography Likelihood-enhanced Fast Rotation Functions , 2003 .

[10]  Jianpeng Ma,et al.  Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution. , 2007, Structure.

[11]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[12]  P. Adams,et al.  Substructure search procedures for macromolecular structures. , 2003, Acta crystallographica. Section D, Biological crystallography.

[13]  David Baker,et al.  Prospects for de novo phasing with de novo protein models , 2009, Acta crystallographica. Section D, Biological crystallography.

[14]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.

[15]  Gérard Bricogne,et al.  SHARP: maximum-likelihood refinement of heavy-atom parameters in the MIR and MAD methods , 1996 .

[16]  T. A. Jones,et al.  The Uppsala Electron-Density Server. , 2004, Acta crystallographica. Section D, Biological crystallography.

[17]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[18]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[19]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[20]  G. Bricogne,et al.  Exploiting the anisotropy of anomalous scattering boosts the phasing power of SAD and MAD experiments , 2008, Acta crystallographica. Section D, Biological crystallography.

[21]  Randy J. Read,et al.  Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .

[22]  B. Delabarre,et al.  Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains , 2003, Nature Structural Biology.

[23]  P. Adams,et al.  Electronic Reprint Biological Crystallography a Robust Bulk-solvent Correction and Anisotropic Scaling Procedure Afonine Et Al. ¯ Bulk-solvent Correction and Anisotropic Scaling Biological Crystallography a Robust Bulk-solvent Correction and Anisotropic Scaling Procedure , 2004 .

[24]  K D Cowtan,et al.  Phase combination and cross validation in iterated density-modification calculations. , 1996, Acta crystallographica. Section D, Biological crystallography.

[25]  Claus-Wilhelm von der Lieth,et al.  GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages , 2007, Nucleic Acids Res..

[26]  Randy J. Read,et al.  Pushing the boundaries of molecular replacement with maximum likelihood. , 2001, Acta crystallographica. Section D, Biological crystallography.

[27]  Helen M Berman,et al.  RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). , 2008, RNA.

[28]  Ronan M Keegan,et al.  Automated search-model discovery and preparation for structure solution by molecular replacement. , 2007, Acta crystallographica. Section D, Biological crystallography.

[29]  Thomas C Terwilliger,et al.  Using prime-and-switch phasing to reduce model bias in molecular replacement. , 2004, Acta crystallographica. Section D, Biological crystallography.

[30]  M. Zalis,et al.  Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. , 1999, Journal of molecular biology.

[31]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[32]  G. Bricogne,et al.  Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. , 2004, Acta crystallographica. Section D, Biological crystallography.

[33]  Roland L. Dunbrack Rotamer libraries in the 21st century. , 2002, Current opinion in structural biology.

[34]  Randy J. Read,et al.  Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias , 2008, Acta crystallographica. Section D, Biological crystallography.

[35]  Raul Cachau,et al.  Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase , 2008, Proceedings of the National Academy of Sciences.

[36]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[37]  Randy J Read,et al.  Simple algorithm for a maximum-likelihood SAD function. , 2004, Acta crystallographica. Section D, Biological crystallography.

[38]  Thomas C. Terwilliger,et al.  Automated MAD and MIR structure solution , 1999, Acta crystallographica. Section D, Biological crystallography.

[39]  R. Read,et al.  Improved Structure Refinement Through Maximum Likelihood , 1996 .

[40]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Likelihood-enhanced Fast Translation Functions Biological Crystallography Likelihood-enhanced Fast Translation Functions , 2022 .

[41]  A. Brünger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures , 1992, Nature.

[42]  Sean McSweeney,et al.  Specific radiation damage can be used to solve macromolecular crystal structures. , 2003, Structure.

[43]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[44]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[45]  P. Bradley,et al.  High-resolution structure prediction and the crystallographic phase problem , 2007, Nature.

[46]  Axel T. Brunger,et al.  X-ray structure determination at low resolution , 2009 .

[47]  Eleanor J. Dodson,et al.  Computational biology: Protein predictions , 2007, Nature.

[48]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[49]  D. Sayre The squaring method: a new method for phase determination , 1952 .

[50]  Karsten Suhre,et al.  On the potential of normal-mode analysis for solving difficult molecular-replacement problems. , 2004, Acta crystallographica. Section D, Biological crystallography.

[51]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Maximum-likelihood Density Modification , 2022 .

[52]  T A Jones,et al.  Errors and reproducibility in electron-density map interpretation. , 1999, Acta crystallographica. Section D, Biological crystallography.

[53]  Paul D. Adams,et al.  Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules , 2009, Acta crystallographica. Section D, Biological crystallography.

[54]  R J Read,et al.  Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement. , 1999, Acta crystallographica. Section D, Biological crystallography.

[55]  Jeffrey J. Headd,et al.  Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place , 2008, Journal of Structural and Functional Genomics.

[56]  Pavol Skubák,et al.  Direct incorporation of experimental phase information in model refinement. , 2004, Acta crystallographica. Section D, Biological crystallography.

[57]  Fei Long,et al.  BALBES: a molecular-replacement pipeline , 2007, Acta crystallographica. Section D, Biological crystallography.

[58]  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.

[59]  Paul D. Adams,et al.  A robust bulk-solvent correction and anisotropic scaling procedure , 2005, Acta crystallographica. Section D, Biological crystallography.

[60]  Adam Godzik,et al.  The importance of alignment accuracy for molecular replacement. , 2004, Acta crystallographica. Section D, Biological crystallography.

[61]  Serge X. Cohen,et al.  Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 , 2008, Nature Protocols.

[62]  C. Dumas,et al.  Macromolecular structure solution by charge flipping. , 2008, Acta crystallographica. Section D, Biological crystallography.

[63]  Kevin Cowtan Generic representation and evaluation of properties as a function of position in reciprocal space , 2002 .

[64]  J. Abrahams,et al.  Methods used in the structure determination of bovine mitochondrial F1 ATPase. , 1996, Acta crystallographica. Section D, Biological crystallography.

[65]  Shuren Wang,et al.  A test of enhancing model accuracy in high-throughput crystallography , 2005, Journal of Structural and Functional Genomics.

[66]  R. Read New ways of looking at experimental phasing. , 2003, Acta crystallographica. Section D, Biological crystallography.

[67]  Gábor Oszlányi,et al.  The charge flipping algorithm. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[68]  G N Murshudov,et al.  Use of TLS parameters to model anisotropic displacements in macromolecular refinement. , 2001, Acta crystallographica. Section D, Biological crystallography.