Phenix.model-vs-data: A high-level tool for the calculation of crystallographic model and data statistics

Journal of Applied Crystallography

Volumn 43, Issue 4, 2010, Pages 669-676

  Afonine, Pavel V ^a   Grosse Kunstleve, Ralf W ^a   Chen, Vincent B ^b   Headd, Jeffrey J ^b   Moriarty, Nigel W ^a   Richardson, Jane S ^b   Richardson, David C ^b   Urzhumtsev, Alexandre ^c,d   Zwart, Peter H ^a   Adams, Paul D ^a,e  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

^c INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^d UNIVERSITÉ DE LORRAINE   (France)

^e University of California at Berkeley   (United States)

Author keywords

data quality; model quality; PHENIX; Protein Data Bank; R factors; structure validation

Indexed keywords

EID: 77954522769     PISSN: 00218898     EISSN: 16005767     Source Type: Journal    
DOI: 10.1107/S0021889810015608     Document Type: Article

References (52)

1. Adams P. D. et al. (2010). Acta Cryst. D66 213-221.
2. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K. & Terwilliger, T. C. (2002). Acta Cryst. D58, 1948-1954.
3. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005a). CCP4 Newsletter, No.42.
4. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005b). Acta Cryst. D61, 850-855.
5. Afonine, P. V., Grosse-Kunstleve, R. W., Adams, P. D., Lunin, V. Y. & Urzhumtsev, A. (2007). Acta Cryst. D63, 1194-1197.
6. Afonine, P. V., Lunin, V. Y., Muzet, N. & Urzhumtsev, A. (2004). Acta Cryst. D60, 260-274.
7. Allen, F. H. (1986). Acta Cryst. B42, 515-522.
8. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.
9. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). J. Mol. Biol. 112, 535-542.
10. Brünger, A. T. (1992). Nature (London), 355, 472-475.
11. Brünger, A. T. (2007). Nat. Protoc. 2, 2728-2733.
12. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
13. Burling, F. T. & Brünger, A. T. (1994). Israel J. Chem. 34, 165-175.
14. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
15. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
16. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B. III, Snoeyink, J., Richardson, J. S. & Richardson, D. C. (2007). Nucleic Acids Res. 35, W375-W383.
17. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
18. Fokine, A. & Urzhumtsev, A. (2002). Acta Cryst. D58, 1387-1392.
19. Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 126-136.
20. Hansen, N. K. & Coppens, P. (1978). Acta Cryst. A34, 909-921.
21. Helliwell, J. R. (2008). Crystallogr. Rev. 14, 189-250.
22. Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100-115.
23. Joosten, R. P., Salzemann, J. et al. (2009). J. Appl. Cryst. 42, 376-384.
24. Joosten, R. P., Womack, T., Vriend, G. & Bricogne, G. (2009). Acta Cryst. D65, 176-185.
25. Kleywegt, G. J., Harris, M. R., Zou, J., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). Acta Cryst. D60, 2240-2249.
26. Lebedev, A. A., Vagin, A. A. & Murshudov, G. N. (2006). Acta Cryst. D62, 83-95.
27. Levin, E. J., Kondrashov, D. A., Wesenberg, G. E. & Phillips, G. N. Jr (2007). Structure, 15, 1040-1052.
28. Lovell, S. C., Davis, I. W., Arendall, W. B. III, de Bakker, P. I. W., Word, J. M., Prisant, M. J., Richardson, J. S. & Richardson, D. C. (2003). Proteins Struct. Func. Genet. 50, 437-450.
29. Lovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. (2000). Proteins Struct. Func. Genet. 40, 389-408.
30. Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. (2009). Acta Cryst. D65, 1074-1080.
31. Murshudov, G. N., Davies, G. J., Isupov, M., Krzywda, S. & Dodson, E. J. (1998). CCP4 Newsl. Protein Crystallogr. 35, 37-43.
32. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
33. Niimura, N., Arai, S., Kurihara, K., Chatake, T., Tanaka, I. & Bau, R. (2006). Cell. Mol. Life Sci. 63, 285-300.
34. Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.
35. Parkin, S., Moezzi, B. & Hope, H. (1995). J. Appl. Cryst. 28, 53-56.
36. Parsons, S. (2003). Acta Cryst. D59, 1995-2003.
37. Praznikar, J., Afonine, P. V., Guncar, G., Adams, P. D. & Turk, D. (2009). Acta Cryst. D65, 921-931.
38. Read, R. J. (1986). Acta Cryst. A42, 140-149.
39. Read, R. J. (1999). Acta Cryst. D55, 1759-1764.
40. Schomaker, V. & Trueblood, K. N. (1968). Acta Cryst. B24, 63-76.
41. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
42. Sheriff, S. & Hendrickson, W. A. (1987). Acta Cryst. A43, 118-121.
43. Terwilliger, T. C. & Berendzen, J. (1995). Acta Cryst. D51, 609-618.
44. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Adams, P. D., Moriarty, N. W., Zwart, P., Read, R. J., Turk, D. & Hung, L.-W. (2007). Acta Cryst. D63, 597-610.
45. Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). Acta Cryst. A43, 489-501.
46. Urzhumtsev, A. G., Skovoroda, T. P. & Lunin, V. Y. (1996). J. Appl. Cryst. 29, 741-744.
47. Urzhumtseva, L., Afonine, P. V., Adams, P. D. & Urzhumtsev, A. (2009). Acta Cryst. D65, 297-300.
48. Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H. J. & Sheldrick, G. M. (1999). Acta Cryst. D55, 1158-1167.
49. Vagin, A. A. & Murshudov, G. N. (2004). IUCr Commission on Crystallographic Computing Newsletter, No.4, pp. 59-72.
50. Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N. (2004). Acta Cryst. D60, 2184-2195.
51. Word, J. M., Lovell, S. C., LaBean, T. H., Taylor, H. C., Zalis, M. E., Presley, B. K., Richardson, J. S. & Richardson, D. C. (1999). J. Mol. Biol. 285, 1711-1733.
52. Zwart, P. H., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). CCP4 Newsl. No.43, contribution 7.