Improved crystallographic structures using extensive combinatorial refinement

Structure

Volumn 21, Issue 11, 2013, Pages 1923-1930

  Nwachukwu, Jerome C ^a   Southern, Mark R ^a   Kiefer, James R ^b   Afonine, Pavel V ^c   Adams, Paul D ^c,d   Terwilliger, Thomas C ^e   Nettles, Kendall W ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b GENENTECH INC   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d University of California at Berkeley   (United States)

^e LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CONFORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; EXTENSIVE COMBINATORIAL REFINEMENT; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ESTROGEN RECEPTOR ALPHA; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; SOFTWARE;

EID: 84887410762     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.07.025     Document Type: Article

References (37)

1. P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.W. Hung, G.J. Kapral, and R.W. Grosse-Kunstleve PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
2. P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, N. Echols, J.J. Headd, L.W. Hung, S. Jain, G.J. Kapral, and R.W. Grosse Kunstleve The Phenix software for automated determination of macromolecular structures Methods 55 2011 94 106
3. P.V. Afonine, R.W. Grosse-Kunstleve, N. Echols, J.J. Headd, N.W. Moriarty, M. Mustyakimov, T.C. Terwilliger, A. Urzhumtsev, P.H. Zwart, and P.D. Adams Towards automated crystallographic structure refinement with phenix.refine Acta Crystallogr. D Biol. Crystallogr. 68 2012 352 367
4. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
5. A.T. Brünger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Nature 355 1992 472 475
6. A.T. Brunger, D. Das, A.M. Deacon, J. Grant, T.C. Terwilliger, R.J. Read, P.D. Adams, M. Levitt, and G.F. Schröder Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum Acta Crystallogr. D Biol. Crystallogr. 68 2012 391 403
7. J.B. Bruning, A.A. Parent, G. Gil, M. Zhao, J. Nowak, M.C. Pace, C.L. Smith, P.V. Afonine, P.D. Adams, J.A. Katzenellenbogen, and K.W. Nettles Coupling of receptor conformation and ligand orientation determine graded activity Nat. Chem. Biol. 6 2010 837 843
8. B.T. Burnley, P.V. Afonine, P.D. Adams, and P. Gros Modelling dynamics in protein crystal structures by ensemble refinement Elife 1 2012 e00311
9. V.B. Chen, W.B. Arendall III, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D Biol. Crystallogr. 66 2010 12 21
10. M.A. DePristo, P.I. de Bakker, and T.L. Blundell Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography Structure 12 2004 831 838
11. M.A. Depristo, P.I. de Bakker, R.J. Johnson, and T.L. Blundell Crystallographic refinement by knowledge-based exploration of complex energy landscapes Structure 13 2005 1311 1319
12. F. DiMaio, T.C. Terwilliger, R.J. Read, A. Wlodawer, G. Oberdorfer, U. Wagner, E. Valkov, A. Alon, D. Fass, and H.L. Axelrod Improved molecular replacement by density- and energy-guided protein structure optimization Nature 473 2011 540 543
13. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
14. N. Furnham, A.S. Doré, D.Y. Chirgadze, P.I. de Bakker, M.A. Depristo, and T.L. Blundell Knowledge-based real-space explorations for low-resolution structure determination Structure 14 2006 1313 1320
15. R.P. Joosten, J. Salzemann, V. Bloch, H. Stockinger, A.C. Berglund, C. Blanchet, E. Bongcam-Rudloff, C. Combet, A.L. Da Costa, and G. Deleage PDB-REDO: automated re-refinement of X-ray structure models in the PDB J. Appl. Cryst. 42 2009 376 384
16. R.P. Joosten, T. Womack, G. Vriend, and G. Bricogne Re-refinement from deposited X-ray data can deliver improved models for most PDB entries Acta Crystallogr. D Biol. Crystallogr. 65 2009 176 185
17. G.J. Kleywegt Use of non-crystallographic symmetry in protein structure refinement Acta Crystallogr. D Biol. Crystallogr. 52 1996 842 857
18. G.J. Kleywegt Separating model optimization and model validation in statistical cross-validation as applied to crystallography Acta Crystallogr. D Biol. Crystallogr. 63 2007 939 940
19. G.J. Kleywegt, and A.T. Brünger Checking your imagination: applications of the free R value Structure 4 1996 897 904
20. P.T. Lang, H.L. Ng, J.S. Fraser, J.E. Corn, N. Echols, M. Sales, J.M. Holton, and T. Alber Automated electron-density sampling reveals widespread conformational polymorphism in proteins Protein Sci. 19 2010 1420 1431
21. G. Langer, S.X. Cohen, V.S. Lamzin, and A. Perrakis Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Nat. Protoc. 3 2008 1171 1179
22. S. McNicholas, E. Potterton, K.S. Wilson, and M.E. Noble Presenting your structures: the CCP4mg molecular-graphics software Acta Crystallogr. D Biol. Crystallogr. 67 2011 386 394
23. Z. Otwinowski, and W. Minor Processing of X-ray Diffraction Data Collected in Oscillation Mode Methods Enzymol. 276 1997 307 326
24. J. Painter, and E.A. Merritt Optimal description of a protein structure in terms of multiple groups undergoing TLS motion Acta Crystallogr. D Biol. Crystallogr. 62 2006 439 450
25. J. Painter, and E.A. Merritt TLSMD web server for the generation of multi-group TLS models J. Appl. Crystallogr. 39 2006 109 111
26. R.J. Read, P.D. Adams, W.B. Arendall III, A.T. Brunger, P. Emsley, R.P. Joosten, G.J. Kleywegt, E.B. Krissinel, T. Lütteke, and Z. Otwinowski A new generation of crystallographic validation tools for the protein data bank Structure 19 2011 1395 1412
27. L.M. Rice, Y. Shamoo, and A.T. Brunger Phase improvement by multi-start simulated annealing refinement and structure-factor averaging J. Appl. Crystallogr. 31 1998 798 805
28. C.A. Rohl, C.E. Strauss, K.M. Misura, and D. Baker Protein structure prediction using Rosetta Methods Enzymol. 383 2004 66 93
29. G.F. Schröder, M. Levitt, and A.T. Brunger Super-resolution biomolecular crystallography with low-resolution data Nature 464 2010 1218 1222
30. A.W. Schüttelkopf, and D.M. van Aalten PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60 2004 1355 1363
31. M. Strong, M.R. Sawaya, S. Wang, M. Phillips, D. Cascio, and D. Eisenberg Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis Proc. Natl. Acad. Sci. USA 103 2006 8060 8065
32. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, P.D. Adams, N.W. Moriarty, P. Zwart, R.J. Read, D. Turk, and L.W. Hung Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models Acta Crystallogr. D Biol. Crystallogr. 63 2007 597 610
33. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.H. Zwart, L.W. Hung, R.J. Read, and P.D. Adams Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Acta Crystallogr. D Biol. Crystallogr. 64 2008 61 69
34. L. Urzhumtseva, P.V. Afonine, P.D. Adams, and A. Urzhumtsev Crystallographic model quality at a glance Acta Crystallogr. D Biol. Crystallogr. 65 2009 297 300
35. H. van den Bedem, A. Dhanik, J.C. Latombe, and A.M. Deacon Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers Acta Crystallogr. D Biol. Crystallogr. 65 2009 1107 1117
36. C. Vonrhein, E. Blanc, P. Roversi, and G. Bricogne Automated structure solution with autoSHARP Methods Mol. Biol. 364 2007 215 230
37. M.D. Winn, C.C. Ballard, K.D. Cowtan, E.J. Dodson, P. Emsley, P.R. Evans, R.M. Keegan, E.B. Krissinel, A.G. Leslie, and A. McCoy Overview of the CCP4 suite and current developments Acta Crystallogr. D Biol. Crystallogr. 67 2011 235 242