Towards automated crystallographic structure refinement with phenix.refine

Acta Crystallographica Section D: Biological Crystallography

Volumn 68, Issue 4, 2012, Pages 352-367

  Afonine, Pavel V ^a   Grosse Kunstleve, Ralf W ^a   Echols, Nathaniel ^a   Headd, Jeffrey J ^a   Moriarty, Nigel W ^a   Mustyakimov, Marat ^b   Terwilliger, Thomas C ^b   Urzhumtsev, Alexandre ^c,d   Zwart, Peter H ^a   Adams, Paul D ^a,e  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (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

joint X ray neutron refinement; maximum likelihood; NCS Model building, refinement and validation; PHENIX; real space refinement; simulated annealing; structure refinement; subatomic resolution; TLS; twinning

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; METHODOLOGY; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; SOFTWARE;

EID: 84860273177     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444912001308     Document Type: Article

References (142)

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. Adams, P. D., Mustyakimov, M., Afonine, P. V. & Langan, P. (2009). Acta Cryst. D65, 567-573.
4. Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Proc. Natl Acad. Sci. USA, 94, 5018-5023.
5. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005a). Acta Cryst. D61, 850-855.
6. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005b). CCP4 Newsl. Protein Crystallogr. 42, contribution 8.
7. Afonine, P. V., Grosse-Kunstleve, R. W., Adams, P. D., Lunin, V. Y. & Urzhumtsev, A. (2007). Acta Cryst. D63, 1194-1197.
8. Afonine, P. V., Grosse-Kunstleve, R. W., Urzhumtsev, A. & Adams, P. D. (2009). J. Appl. Cryst. 42, 607-615.
9. Afonine, P. V., Lunin, V. Y., Muzet, N. & Urzhumtsev, A. (2004). Acta Cryst. D60, 260-274.
10. Afonine, P. V., Mustyakimov, M., Grosse-Kunstleve, R. W., Moriarty, N. W., Langan, P. & Adams, P. D. (2010). Acta Cryst. D66, 1153-1163.
11. Afonine, P. V. & Urzhumtsev, A. (2004). Acta Cryst. A60, 19-32.
12. Afonine, P. V., Urzhumtsev, A., Grosse-Kunstleve, R. W. & Adams, P. D. (2010). Comput. Crystallogr. Newsl. 1, 24-31.
13. Afonine, P. V., Urzhumtsev, A., Grosse-Kunstleve, R. W. & Adams, P. D. (2011). Comput. Crystallogr. Newsl. 2, 99-103.
14. Agarwal, R. C. (1978). Acta Cryst. A34, 791-809.
15. Berman, H. M., Olson,W. K., Beveridge, D. L.,Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R. & Schneider, B. (1992). Biophys. J. 63, 751-759.
16. 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.
17. 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.
18. Bourne, Y., Talley, T. T., Hansen, S. B., Taylor, P. &Marchot, P. (2005). EMBO J. 24, 1512-1522.
19. Braig, K., Adams, P. D. & Brünger, A. T. (1995). Nature Struct. Biol. 2, 1083-1094.
20. Bricogne, G. & Irwin, J. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M.
21. Moore, A. Ralph & S. Bailey, pp. 85-92. Warrington: Daresbury Laboratory.
22. Brouillette, C. G. & Anantharamaiah, G. M. (1995). Biochim. Biophys. Acta, 1256, 103-129.
23. Brünger, A. T. 1992 Nature (London) 355 472-475
24. Brünger, A. T. 1993 Acta Cryst. D49 24-36.
25. Brunger, A. T. (2007). Nature Protoc. 2, 2728-2733.
26. Brunger, A. T. & Adams, P. D. (2002). Acc. Chem. Res. 35, 404-412.
27. 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.
28. Brunger, A. T., Adams, P. D. & Rice, L. M. (2001). International Tables for Crystallography, Vol. F, edited by M. G. Rossmann & E. Arnold, pp. 375-381. Dordrecht: Kluwer Academic Publishers.
29. Brunger, A. T., DeLaBarre, B., Davies, J. M. & Weis, W. I. (2009). Acta Cryst. D65, 128-133.
30. Brünger, A. T., Karplus, M. & Petsko, G. A. (1989). Acta Cryst. A45, 50-61.
31. Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Science, 235, 458-460.
32. Chapman, M. S. (1995). Acta Cryst. A51, 69-80.
33. Chatani, E., Hayashi, R.,Moriyama, H. & Ueki, T. (2002). Protein Sci. 11, 72-81.
34. Cheetham, J. C., Artymiuk, P. J. & Phillips, D. C. (1992). J. Mol. Biol. 224, 613-628.
35. 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.
36. Clayton, A., Siebold, C., Gilbert, R. J., Sutton, G. C., Harlos, K., McIlhinney, R. A., Jones, E. Y. & Aricescu, A. R. (2009). J. Mol. Biol. 392, 1125-1132.
37. Coppens, P., Boehme, R., Price, P. F. & Stevens, E. D. (1981). Acta Cryst. A37, 857-863.
38. Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1995). Curr. Opin. Struct. Biol. 5, 784-790.
39. Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1997). Curr. Opin. Struct. Biol. 7, 681-688.
40. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J., Richardson, J. S. & Richardson, D. C. (2007). Nucleic Acids Res. 35, W375-W383.
41. Deisenhofer, J., Remington, S. J. & Steigemann, W. (1985). Methods Enzymol. 115, 303-323.
42. DeLaBarre, B. & Brunger, A. T. (2006). Acta Cryst. D62, 923-932.
43. DeLano, W. L. (2002). PyMOL. http://www.pymol.org.
44. Diamond, R. (1971). Acta Cryst. A27, 436-452.
45. Dunitz, J. D. & White, D. N. J. (1973). Acta Cryst. A29, 93-94.
46. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
47. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
48. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
49. Fokine, A. & Urzhumtsev, A. (2002). Acta Cryst. D58, 1387-1392.
50. French, S. & Wilson, K. (1978). Acta Cryst. A34, 517-525.
51. Grosse-Kunstleve, R. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 477-480.
52. Grosse-Kunstleve, R.W. & Adams, P. D. (2010). Comput. Crystallogr. Newsl. 1, 4-11.
53. Grosse-Kunstleve, R. W., Afonine, P. V. & Adams, P. D. (2004). IUCr Comput. Comm. Newsl. 4, 19-36.
54. Grosse-Kunstleve, R. W., Afonine, P. V., Sauter, N. K. & Adams, P. D. (2005). IUCr Comput. Comm. Newsl. 5, 69-91.
55. Grosse-Kunstleve, R. W., Moriarty, N. W. & Adams, P. D. (2009). ASME Conf. Proc. 4, 1477-1485.
56. Grosse-Kunstleve, R. W., Sauter, N. K. & Adams, P. D. (2004). IUCr Comput. Comm. Newsl. 3, 22-31.
57. Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 126-136.
58. Grosse-Kunstleve, R. W., Wong, B., Mustyakimov, M. & Adams, P. D. (2011). Acta Cryst. A67, 269-275.
59. Guillot, B., Lecomte, C., Cousson, A., Scherf, C. & Jelsch, C. (2001). Acta Cryst. D57, 981-989.
60. Guncar, G., Klemencic, I., Turk, B., Turk, V., Karaoglanovic Carmona, A., Juliano, L. & Turk, D. (2000). Structure, 8, 305-313.
61. Habash, J., Raftery, J., Nuttall, R., Price, H. J., Wilkinson, C., Kalb (Gilboa), A. J. & Helliwell, J. R. (2000). Acta Cryst. D56, 541-550.
62. Headd, J. J., Echols, N., Afonine, P. V., Grosse-Kunstleve, R.W., Chen, V. B., Moriarty, N. W., Richardson, D. C., Richardson, J. S. & Adams, P. D. (2012). Acta Cryst. D68, 381-390.
63. Helliwell, J. R. (2008). Crystallogr. Rev. 14, 189-250.
64. Hendrickson, W. A. (1985). Methods Enzymol. 115, 252-270.
65. Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
66. Janssen, B. J., Christodoulidou, A., McCarthy, A., Lambris, J. D. & Gros, P. (2006). Nature (London), 444, 213-216.
67. Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100-115.
68. Johnson, C. K. & Levy, H. A. (1974). International Tables for X-ray Crystallography, Vol. IV, edited by J. A. Ibers & W. C. Hamilton, pp. 311-335. Birmingham: Kynoch Press.
69. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
70. Joosten, R. P. et al. (2009). J. Appl. Cryst. 42, 376-384.
71. Kleywegt, G. J. (1996). Acta Cryst. D52, 842-857.
72. Kleywegt, G. J. (1999). Acta Cryst. D55, 1878-1884.
73. Kleywegt, G. J. (2001). International Tables for Crystallography, Vol. F, edited by M. G. Rossmann & E. Arnold, ch. 21.1. Dordrecht: Kluwer Academic Publishers.
74. Kleywegt, G. J. & Jones, T. A. (1995). Structure, 3, 535-540.
75. Korostelev, A., Bertram, R. & Chapman, M. S. (2002). Acta Cryst. D58, 761-767.
76. Li, S., Wang, H., Peng, B., Zhang, M., Zhang, D., Hou, S., Guo, Y. & Ding, J. (2009). Proc. Natl Acad. Sci. USA, 106, 4349-4354.
77. Liu, D. C. & Nocedal, J. (1989). Math. Program. 45, 503-528.
78. Lunin, V. Yu. (1988). Acta Cryst. A44, 144-150.
79. Lunin, V. Y., Afonine, P. V. & Urzhumtsev, A. G. (2002). Acta Cryst. A58, 270-282.
80. Lunina, N. L., Lunin, V. Y. & Podjarny, A. D. (2002). CCP4 Newsl. Protein Crystallogr. 41, contribution 10.
81. Lunin, V. Yu. & Skovoroda, T. P. (1991). Acta Cryst. A47, 45-52.
82. Lunin, V. Yu. & Skovoroda, T. P. (1995). Acta Cryst. A51, 880-887.
83. Lunin, V. Yu. & Urzhumtsev, A. G. (1984). Acta Cryst. A40, 269-277.
84. Maslen, E. N., Fox, A. G. & O'Keefe, M. A. (1992). International Tables for Crystallography, Vol. C, edited by A. J. C. Wilson, pp. 476-516. Dordrecht: Kluwer Academic Publishers.
85. Moriarty, N.W., Grosse-Kunstleve, R.W. & Adams, P. D. (2009). Acta Cryst. D65, 1074-1080.
86. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
87. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
88. Neutron News (1992). Vol. 3, No. 3, pp. 29-37.
89. Ohishi, H., Tozuka, Y., Da-Yang, Z., Ishida, T. & Nakatani, K. (2007). Biochem. Biophys. Res. Commun. 358, 24-28.
90. Oldfield, T. J. (2001). Acta Cryst. D57, 82-94.
91. Otwinowski, Z. & Minor,W. (1997). Methods Enzymol. 276, 307-326.
92. Painter, J. & Merritt, E. A. (2006a). Acta Cryst. D62, 439-450.
93. Painter, J. & Merritt, E. A. (2006b). J. Appl. Cryst. 39, 109-111.
94. Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J. (1998). Acta Cryst. D54, 1285-1294.
95. Pannu, N. S. & Read, R. J. (1996). Acta Cryst. A52, 659-668.
96. Parsons, S. (2003). Acta Cryst. D59, 1995-2003.
97. Petrova, T. E. & Podjarny, A. D. (2004). Rep. Prog. Phys. 67, 1565-1605.
98. Phillips, S. E. (1980). J. Mol. Biol. 142, 531-554.
99. Pražnikar, J., Afonine, P. V., Gunčar, G., Adams, P. D. & Turk, D. (2009). Acta Cryst. D65, 921-931.
100. Prince, E. & Finger, L. W. (1973). Acta Cryst. B29, 179-183.
101. Qiu, C., Tarrant, M. K., Choi, S. H., Sathyamurthy, A., Bose, R., Banjade, S., Pal, A., Bornmann, W. G., Lemmon, M. A., Cole, P. A. & Leahy, D. J. (2008). Structure, 16, 460-467.
102. Read, R. J. (1986). Acta Cryst. A42, 140-149.
103. Read, R. J. (1990). Acta Cryst. A46, 900-912.
104. Read, R. J. (1999). Acta Cryst. D55, 1759-1764.
105. Rice, L. M. & Brünger, A. T. (1994). Proteins, 19, 277-290.
106. Roach, J. (2003). Methods Enzymol. 374, 137-145.
107. Rose, R. B., Endrizzi, J. A., Cronk, J. D., Holton, J. & Alber, T. (2000). Biochemistry, 39, 15062-15070.
108. Satyshur, K. A., Worzalla, G. A., Meyer, L. S., Heiniger, E. K., Aukema, K. G., Misic, A. M. & Forest, K. T. (2007). Structure, 15, 363-376.
109. Schneider, T. R. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 133-144.Warrington: Daresbury Laboratory.
110. Schomaker, V. & Trueblood, K. N. (1968). Acta Cryst. B24, 63-76.
111. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
112. Sheldrick, G. M. & Schneider, T. R. (1997). Methods Enzymol. 277, 319-343.
113. Sheriff, S. & Hendrickson, W. A. (1987). Acta Cryst. A43, 118-121.
114. Stuart, D. I. & Phillips, D. C. (1985). Methods Enzymol. 115, 117-142.
115. Sutton, R. B., Ernst, J. A. & Brunger, A. T. (1999). J. Cell Biol. 147, 589-598.
116. Szep, S., Park, S., Boder, E. T., Van Duyne, G. D. & Saven, J. G. (2009). Proteins, 74, 603-611.
117. 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.
118. Tronrud, D. E. (1994). Proceedings of the CCP4 Study Weekend. From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. Waller, pp. 111-124. Warrington: Daresbury Laboratory.
119. Tronrud, D. W. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 1-10. Warrington: Daresbury Laboratory.
120. Tronrud, D. E. (1997). Methods Enzymol. 277, 306-319.
121. Tsukimoto, K., Takada, R., Araki, Y., Suzuki, K., Karita, S., Wakagi, T., Shoun, H.,Watanabe, T. & Fushinobu, S. (2010). FEBS Lett. 584, 1205-1211.
122. Turk, D. (2007). Evolving Methods for Macromolecular Crystallography, edited by R. J. Read & J. L. Sussman, pp. 111-122. New York: Springer.
123. Urzhumtsev, A., Afonine, P. V. & Adams, P. D. (2009). Acta Cryst. D65, 1283-1291.
124. Urzhumtsev, A., Afonine, P. V. & Adams, P. D. (2011). Comput. Crystallogr. Newsl. 2, 42-84.
125. Urzhumtsev, A. G., Lunin, V. Yu. & Luzyanina, T. B. (1989). Acta Cryst. A45, 34-39.
126. Urzhumtsev, A. G., Lunin, V. Yu. & Vernoslova, E. A. (1989). J. Appl. Cryst. 22, 500-506.
127. Urzhumtsev, A. G., Skovoroda, T. P. & Lunin, V. Y. (1996). J. Appl. Cryst. 29, 741-744.
128. Urzhumtseva, L., Afonine, P. V., Adams, P. D. & Urzhumtsev, A. (2009). Acta Cryst. D65, 297-300.
129. Urzhumtseva, L. & Urzhumtsev, A. (2011). J. Appl. Cryst. 44, 865-872.
130. Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H. J. & Sheldrick, G. M. (1999). Acta Cryst. D55, 1158-1167.
131. Vagin, A. A. & Murshudov, G. N. (2004). IUCr Comput. Comm. Newsl. 4, 59-72.
132. Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N. (2004). Acta Cryst. D60, 2184-2195.
133. Vedadi, M. et al. (2007). Mol. Biochem. Parasitol. 151, 100-110.
134. Volkov, A., Messerschmidt, M. & Coppens, P. (2007). Acta Cryst. D63, 160-170.
135. Vrielink, A. & Sampson, N. (2003). Curr. Opin. Struct. Biol. 13, 709-715.
136. Wang, J., Meijers, R., Xiong, Y., Liu, J., Sakihama, T., Zhang, R., Joachimiak, A. & Reinherz, E. L. (2001). Proc. Natl Acad. Sci. USA, 98, 10799-10804.
137. Waasmaier, D. & Kirfel, A. (1995). Acta Cryst. A51, 416-431.
138. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
139. Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001). Acta Cryst. D57, 122-133.
140. Wlodawer, A. & Hendrickson, W. A. (1981). Acta Cryst. A37, C8.
141. Wlodawer, A. & Hendrickson, W. A. (1982). Acta Cryst. A38, 239-247.
142. Zwart, P. H., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). CCP4 Newsl. Protein Crystallogr. 43, contribution 7.