A new generation of crystallographic validation tools for the Protein Data Bank

Structure

Volumn 19, Issue 10, 2011, Pages 1395-1412

  Read, Randy J ^a   Adams, Paul D ^b   Arendall III, W Bryan ^c   Brunger, Axel T ^d   Emsley, Paul ^e   Joosten, Robbie P ^f,g   Kleywegt, Gerard J ^h,i   Krissinel, Eugene B ^i,j   Lütteke, Thomas ^f,k   Otwinowski, Zbyszek ^l   Perrakis, Anastassis ^g   Richardson, Jane S ^c   Sheffler, William H ^m   Smith, Janet L ⁿ   Tickle, Ian J ^o   Vriend, Gert ^f   Zwart, Peter H ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d STANFORD UNIVERSITY   (United States)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^g NETHERLANDS CANCER INSTITUTE   (Netherlands)

^h UPPSALA UNIVERSITY   (Sweden)

ⁱ EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^j RUTHERFORD APPLETON LABORATORY   (United Kingdom)

^k JUSTUS LIEBIG UNIVERSITY   (Germany)

^l UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^m UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

ⁿ UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^o ASTEX PHARMACEUTICALS   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; LIGAND; NUCLEIC ACID;

ARTICLE; GEOMETRY; HYDROGEN BOND; MACROMOLECULE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN STRUCTURE; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ADVISORY COMMITTEES; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HYDROGEN BONDING; PROTEIN CONFORMATION; PROTEINS; QUALITY CONTROL; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; X-RAY DIFFRACTION;

EID: 80054078285     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.08.006     Document Type: Article

References (89)

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.V. Afonine, R.W. Grosse-Kunstleve, and P.D. Adams The Phenix refinement framework CCP4 Newsletter 42 2005 contribution 8
3. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, and P.D. Adams phenix.model-vs-data: a high-level tool for the calculation of crystallographic model and data statistics J. Appl. Cryst. 43 2010 669 676
4. F.H. Allen The Cambridge Structural Database: a quarter of a million crystal structures and rising Acta Crystallogr. B 58 2002 380 388 (Pubitemid 135702674)
5. W.B. Arendall 3rd, W. Tempel, J.S. Richardson, W. Zhou, S. Wang, I.W. Davis, Z.-J. Liu, J.P. Rose, W.M. Carson, and M. Luo A test of enhancing model accuracy in high-throughput crystallography J. Struct. Funct. Genomics 6 2005 1 11 (Pubitemid 40898072)
6. D.S. Berkholz, M.V. Shapovalov, R.L. Dunbrack Jr., and P.A. Karplus Conformation dependence of backbone geometry in proteins Structure 17 2009 1316 1325
7. 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 (Pubitemid 30047768)
8. H.M. Berman, K. Henrick, and H. Nakamura Announcing the worldwide Protein Data Bank Nat. Struct. Biol. 10 2003 980 (Pubitemid 37500485)
9. F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi The Protein Data Bank: a computer-based archival file for macromolecular structures J. Mol. Biol. 112 1977 535 542 (Pubitemid 8109216)
10. J.U. Bowie, R. Lüthy, and D. Eisenberg A method to identify protein sequences that fold into a known three-dimensional structure Science 253 1991 164 170 (Pubitemid 21917131)
11. C.-I. Brändén, and T.A. Jones Between objectivity and subjectivity Nature 343 1990 687 689
12. A.T. Brünger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Nature 355 1992 472 475
13. I.J. Bruno, J.C. Cole, M. Kessler, J. Luo, W.D.S. Motherwell, L.H. Purkis, B.R. Smith, R. Taylor, R.I. Cooper, S.E. Harris, and A.G. Orpen Retrieval of crystallographically-derived molecular geometry information J. Chem. Inf. Comput. Sci. 44 2004 2133 2144
14. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
15. G. Chang, C.B. Roth, C.L. Reyes, O. Pornillos, Y.-J. Chen, and A.P. Chen Retraction Science 314 2006 1875
16. V.B. Chen, W.B. Arendall 3rd, 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
17. M. Crispin, D.I. Stuart, and E.Y. Jones Building meaningful models of glycoproteins Nat. Struct. Mol. Biol. 14 2007 354 discussion 354-355
18. J.M. Davies, A.T. Brunger, and W.I. Weis Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change Structure 16 2008 715 726 (Pubitemid 351615011)
19. A.M. Davis, S.J. Teague, and G.J. Kleywegt Applications and limitations of X-ray crystallographic data in structure-based ligand and drug design Angew. Chem. Int. Ed. Engl. 42 2003 2718 2736 (Pubitemid 36813974)
20. I.W. Davis, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes Nucleic Acids Research 32 Web Server Issue 2004 W615 W619
21. A.M. Davis, S.A. St-Gallay, and G.J. Kleywegt Limitations and lessons in the use of X-ray structural information in drug design Drug Discov. Today 13 2008 831 841
22. E.J. Dudewicz, and S.N. Mishra Modern Mathematical Statistics 1988 Wiley New York
23. R.L. Dunbrack Jr., and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681 (Pubitemid 27333069)
24. R.A. Engh, and R. Huber Accurate bond and angle parameters for X-ray protein structure refinement Acta Crystallogr. A 47 1991 392 400
25. R.A. Engh, and R. Huber Structure quality and target parameters M.G. Rossmann, E. Arnold, International Tables for Crystallography, Volume F 2001 Kluwer Academic Publishers Dordrecht, The Netherlands 382 392
26. P.R. Evans Scaling and assessment of data quality Acta Crystallogr. D Biol. Crystallogr. 62 2006 72 82
27. V. De Filippis, C. Sander, and G. Vriend Predicting local structural changes that result from point mutations Protein Eng. 7 1994 1203 1208 (Pubitemid 24319398)
28. S. French, and K. Wilson On the treatment of negative intensity observations Acta Crystallogr. A 34 1978 517 525
29. A. Gelbin, B. Schneider, L. Clowney, S.-H. Hsieh, W.K. Olson, and H.M. Berman Geometric parameters in nucleic acids: sugar and phosphate constituents J. Am. Chem. Soc. 118 1996 519 529 (Pubitemid 26052035)
30. M.A. Hanson, and R.C. Stevens Retraction: Cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0 A resolution Nat. Struct. Mol. Biol. 16 2009 795
31. M.M. Harding Small revisions to predicted distances around metal sites in proteins Acta Crystallogr. D Biol. Crystallogr. 62 2006 678 682 (Pubitemid 43806647)
32. J.J. He, and F.A. Quiocho Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein Protein Sci. 2 1993 1643 1647 (Pubitemid 23294342)
33. J.J. Headd, R.M. Immormino, D.A. Keedy, P. Emsley, D.C. Richardson, and J.S. Richardson Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place J. Struct. Funct. Genomics 10 2009 83 93
34. K. Henrick, Z. Feng, W.F. Bluhm, D. Dimitropoulos, J.F. Doreleijers, S. Dutta, J.L. Flippen-Anderson, J. Ionides, C. Kamada, and E. Krissinel Remediation of the protein data bank archive Nucleic Acids Res. 36 Database issue 2008 D426 D433
35. V.A. Higman, J. Boyd, L.J. Smith, and C. Redfield Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings J. Biomol. NMR 30 2004 327 346 (Pubitemid 40073583)
36. R.W.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272
37. R.W.W. Hooft, C. Sander, and G. Vriend Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures Proteins 26 1996 363 376 (Pubitemid 27024754)
38. B.J.C. Janssen, R.J. Read, A.T. Brünger, and P. Gros Crystallography: crystallographic evidence for deviating C3b structure Nature 448 2007 E1 E2 10.1038/nature06102 discussion E2-E3 (Pubitemid 47236866)
39. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr. A 47 1991 110 119
40. R.P. Joosten, and G. Vriend PDB improvement starts with data deposition Science 317 2007 195 196 (Pubitemid 47076180)
41. 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. Crystallogr. 42 2009 376 384
42. G.J. Kleywegt Validation of protein models from Calpha coordinates alone J. Mol. Biol. 273 1997 371 376 (Pubitemid 27470291)
43. G.J. Kleywegt Validation of protein crystal structures Acta Crystallogr. D Biol. Crystallogr. 56 2000 249 265 (Pubitemid 30147175)
44. G.J. Kleywegt Crystallographic refinement of ligand complexes Acta Crystallogr. D Biol. Crystallogr. 63 2007 94 100 (Pubitemid 46141484)
45. G.J. Kleywegt, and M.R. Harris ValLigURL: a server for ligand-structure comparison and validation Acta Crystallogr. D Biol. Crystallogr. 63 2007 935 938 (Pubitemid 47094577)
46. G.J. Kleywegt, and T.A. Jones Phi/psi-chology: Ramachandran revisited Structure 4 1996 1395 1400 (Pubitemid 27050273)
47. G.J. Kleywegt, and R.J. Read Not your average density Structure 5 1997 1557 1569 (Pubitemid 28051971)
48. G.J. Kleywegt, H. Hoier, and T.A. Jones A re-evaluation of the crystal structure of chloromuconate cycloisomerase Acta Crystallogr. D Biol. Crystallogr. 52 1996 858 863 (Pubitemid 27064311)
49. G.J. Kleywegt, K. Henrick, E.J. Dodson, and D.M.F. van Aalten Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure 11 2003 1051 1059 (Pubitemid 37103067)
50. G.J. Kleywegt, M.R. Harris, J.Y. Zou, T.C. Taylor, A. Wählby, and T.A. Jones The Uppsala Electron-Density Server Acta Crystallogr. D Biol. Crystallogr. 60 2004 2240 2249 (Pubitemid 41742776)
51. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
52. A.A. Lebedev, A.A. Vagin, and G.N. Murshudov Intensity statistics in twinned crystals with examples from the PDB Acta Crystallogr. D Biol. Crystallogr. 62 2006 83 95
53. S.C. Lovell, J.M. Word, J.S. Richardson, and D.C. Richardson The penultimate rotamer library Proteins 40 2000 389 408 (Pubitemid 30624447)
54. S.C. Lovell, I.W. Davis, W.B. Arendall 3rd, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson Structure validation by Calpha geometry:,ψ and Cbeta deviation Proteins 50 2003 437 450 (Pubitemid 36158457)
55. T. Lütteke Analysis and validation of carbohydrate three-dimensional structures Acta Crystallogr. D Biol. Crystallogr. 65 2009 156 168
56. T. Lütteke, and C.W. von der Lieth pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files BMC Bioinformatics 5 2004 69
57. T. Lütteke, M. Frank, and C.W. von der Lieth Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB Nucleic Acids Res. 33 Database issue 2005 D242 D246
58. M.W. MacArthur, and J.M. Thornton Protein side-chain conformation: a systematic variation of χ 1 mean values with resolution - a consequence of multiple rotameric states? Acta Crystallogr. D Biol. Crystallogr. 55 1999 994 1004 (Pubitemid 29235597)
59. N.W. Moriarty, R.W. Grosse-Kunstleve, and P.D. Adams electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation Acta Crystallogr. D Biol. Crystallogr. 65 2009 1074 1080
60. A.L. Morris, M.W. MacArthur, E.G. Hutchinson, and J.M. Thornton Stereochemical quality of protein structure coordinates Proteins 12 1992 345 364
61. T. Nakahara, R. Hashimoto, H. Nakagawa, K. Monde, N. Miura, and S. Nishimura Glycoconjugate Data Bank: Structures - an annotated glycan structure database and N-glycan primary structure verification service Nucleic Acids Res. 36 Database issue 2008 D368 D371
62. J.E. Padilla, and T.O. Yeates A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning Acta Crystallogr. D Biol. Crystallogr. 59 2003 1124 1130 (Pubitemid 36872347)
63. G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brünger, and H.M. Berman New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D Biol. Crystallogr. 52 1996 57 64 (Pubitemid 126512683)
64. S. Parsons Introduction to twinning Acta Crystallogr. D Biol. Crystallogr. 59 2003 1995 2003 (Pubitemid 37399333)
65. J.W. Ponder, and F.M. Richards Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes J. Mol. Biol. 193 1987 775 791 (Pubitemid 17020078)
66. B.K. Poon, R.W. Grosse-Kunstleve, P.H. Zwart, and N.K. Sauter Detection and correction of underassigned rotational symmetry prior to structure deposition Acta Crystallogr. D Biol. Crystallogr. 66 2010 503 513
67. A.N. Popov, and G.P. Bourenkov Choice of data-collection parameters based on statistic modelling Acta Crystallogr. D Biol. Crystallogr. 59 2003 1145 1153 (Pubitemid 36872350)
68. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan Stereochemistry of polypeptide chain configurations J. Mol. Biol. 7 1963 95 99
69. R.J. Read Improved Fourier coefficients for maps using phases from partial structures with errors Acta Crystallogr. A 42 1986 140 149
70. R.J. Read Detecting outliers in non-redundant diffraction data Acta Crystallogr. D Biol. Crystallogr. 55 1999 1759 1764 (Pubitemid 29504431)
71. F.M. Richards Public access to X-ray diffraction data J. Comput. Aided Mol. Des. 2 1988 3 5
72. J.S. Richardson, B. Schneider, L.W. Murray, G.J. Kapral, R.M. Immormino, J.J. Headd, D.C. Richardson, D. Ham, E. Hershkovits, L.D. Williams RNA Ontology Consortium RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution) RNA 14 2008 465 481 (Pubitemid 351397812)
73. N.K. Sauter, and P.H. Zwart Autoindexing the diffraction patterns from crystals with a pseudotranslation Acta Crystallogr. D Biol. Crystallogr. 65 2009 553 559
74. N.K. Sauter, R.W. Grosse-Kunstleve, and P.D. Adams Improved statistics for determining the Patterson symmetry from unmerged diffraction intensities J. Appl. Crystallogr. 39 2006 158 168
75. A.W. Schüttelkopf, and D.M.F. van Aalten PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60 2004 1355 1363 (Pubitemid 41079731)
76. W. Sheffler, and D. Baker RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation Protein Sci. 18 2009 229 239
77. W. Sheffler, and D. Baker RosettaHoles2: a volumetric packing measure for protein structure refinement and validation Protein Sci. 19 2010 1991 1995
78. G.M. Sheldrick, and T.R. Schneider SHELXL: high-resolution refinement Methods Enzymol. 277 1997 319 343 (Pubitemid 27390928)
79. P.E. Stein, A. Boodhoo, G.J. Tyrrell, J.L. Brunton, and R.J. Read Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli Nature 355 1992 748 750
80. D.E. Tronrud, and B.W. Matthews Sorting the chaff from the wheat at the PDB Protein Sci. 18 2009 2 5
81. A.A. Vaguine, J. Richelle, and S.J. Wodak SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model Acta Crystallogr. D Biol. Crystallogr. 55 1999 191 205 (Pubitemid 29053816)
82. A.J.C. Wilson The probability distribution of X-ray intensities Acta Crystallogr. 2 1949 318 321
83. J.M. Word, S.C. Lovell, T.H. LaBean, H.C. Taylor, M.E. Zalis, B.K. Presley, J.S. Richardson, and D.C. Richardson Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms J. Mol. Biol. 285 1999 1711 1733 (Pubitemid 29060466)
84. J.M. Word, S.C. Lovell, J.S. Richardson, and D.C. Richardson Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285 1999 1735 1747 (Pubitemid 29060467)
85. T.O. Yeates Detecting and overcoming crystal twinning Methods Enzymol. 276 1997 344 358 (Pubitemid 27085613)
86. H. Zheng, M. Chruszcz, P. Lasota, L. Lebioda, and W. Minor Data mining of metal ion environments present in protein structures J. Inorg. Biochem. 102 2008 1765 1776
87. P.H. Zwart, R.W. Grosse-Kunstleve, and P.D. Adams Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation CCP4 newsletter 2005 Contribution 7
88. P.H. Zwart, R.W. Grosse-Kunstleve, and P.D. Adams Characterisation of X-ray data sets CCP4 newsletter 2005 Contribution 10
89. P.H. Zwart, R.W. Grosse-Kunstleve, and P.D. Adams Exploring metric symmetry CCP4 newsletter 2006 Contribution 8