Automated identification of elemental ions in macromolecular crystal structures

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 4, 2014, Pages 1104-1114

  Echols, Nathaniel ^a   Morshed, Nader ^a   Afonine, Pavel V ^a   McCoy, Airlie J ^b   Miller, Mitchell D ^c,d   Read, Randy J ^b   Richardson, Jane S ^e   Terwilliger, Thomas C ^f   Adams, Paul D ^g  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^d Joint Center for Structural Genomics   (United States)

^e DUKE UNIVERSITY MEDICAL CENTER   (United States)

^f LOS ALAMOS NATIONAL LABORATORY   (United States)

^g University of California   (United States)

Author keywords

ions; PHENIX; refinement

Indexed keywords

ION; THERMOLYSIN; THROMBIN;

CHEMICAL STRUCTURE; CHEMISTRY; LABORATORY AUTOMATION; PROCEDURES; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

AUTOMATION, LABORATORY; CRYSTALLOGRAPHY, X-RAY; IONS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; THERMOLYSIN; THROMBIN;

EID: 84898722011     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004714001308     Document Type: Article

References (63)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221
2. Afonine, P. V., Echols, N., Grosse-Kunstleve, R. W., Moriarty, N. W. & Adams, P. D. (2011). Comput. Crystallogr. Newsl. 2, 99-103
3. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352-367
4. Allen, F. H. (2002). Acta Cryst. B58, 380-388
5. Axelrod, H. L. et al. (2010). Acta Cryst. F66, 1347-1353
6. Bastidas, A. C., Deal, M. S., Steichen, J. M., Keshwani, M. M., Guo, Y. & Taylor, S. S. (2012). J. Mol. Biol. 422, 215-229
7. 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
8. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). J. Mol. Biol. 112, 535-542
9. Biela, A., Khayat, M., Tan, H., Kong, J., Heine, A., Hangauer, D. & Klebe, G. (2012). J. Mol. Biol. 418, 350-366
10. Brese, N. E. & O'Keeffe, M. (1991). Acta Cryst. B47, 192-197
11. Bricogne, G. (1997). Methods Enzymol. 276, 361-423
12. Brown, I. D. (2009). Chem. Rev. 109, 6858-6919
13. Brown, I. D. & Altermatt, D. (1985). Acta Cryst. B41, 244-247
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. Dauter, Z. & Dauter, M. (2001). Structure, 9, R21-R26
16. Di Cera, E., Guinto, E. R., Vindigni, A., Dang, Q. D., Ayala, Y. M., Wuyi, M. & Tulinsky, A. (1995). J. Biol. Chem. 270, 22089-22092
17. Dokmanić, I., Sikić, M. & Tomić, S. (2008). Acta Cryst. D64, 257-263
18. Echols, N., Moriarty, N. W., Klei, H. E., Afonine, P. V., Bunkóczi, G., Headd, J. J., McCoy, A. J., Oeffner, R. D., Read, R. J., Terwilliger, T. C. & Adams, P. D. (2014). Acta Cryst. D70, 144-154
19. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501
20. Glusker, J. P. (1991). Adv. Protein Chem. 42, 1-76
21. Harding, M. M. (1999). Acta Cryst. D55, 1432-1443
22. Harding, M. M. (2000). Acta Cryst. D56, 857-867
23. Harding, M. M. (2001). Acta Cryst. D57, 401-411
24. Harding, M. M. (2002). Acta Cryst. D58, 872-874
25. Harding, M. M. (2004). Acta Cryst. D60, 849-859
26. Harding, M. M. (2006). Acta Cryst. D62, 678-682
27. Harding, M. M., Nowicki, M. W. & Walkinshaw, M. D. (2010). Crystallogr. Rev. 16, 247-302
28. Headd, J. J., Echols, N., Afonine, P. V., Moriarty, N. W., Gildea, R. J. & Adams, P. D. (2014). Acta Cryst. D70, doi:10.1107/S1399004714003277
29. Holland, D. R., Hausrath, A. C., Juers, D. & Matthews, B. W. (1995). Protein Sci. 4, 1955-1965
30. Hooft, R. W. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Nature (London), 381, 272
31. Joosten, R. P., Joosten, K., Murshudov, G. N. & Perrakis, A. (2012). Acta Cryst. D68, 484-496
32. Joosten, R. P., Womack, T., Vriend, G. & Bricogne, G. (2009). Acta Cryst. D65, 176-185
33. Klein, D. J., Moore, P. B. & Steitz, T. A. (2004). RNA, 10, 1366-1379
34. Knighton, D. R., Zheng, J. H., Ten Eyck, L. F., Ashford, V. A., Xuong, N. H., Taylor, S. S. & Sowadski, J. M. (1991). Science, 253, 407-414
35. La Fortelle, E. de & Bricogne, G. (1997). Methods Enzymol. 276, 472-494
36. Lamzin, V. S. & Wilson, K. S. (1993). Acta Cryst. D49, 129-147
37. Lane, T. W., Saito, M. A., George, G. N., Pickering, I. J., Prince, R. C. & Morel, F. M. M. (2005). Nature (London), 435, 42
38. Lesley, S. A. et al. (2002). Proc. Natl Acad. Sci. USA, 99, 11664-11669
39. Levisson, M. et al. (2012). Proteins, 80, 1545-1559
40. Lunin, V. Y. & Skovoroda, T. P. (1995). Acta Cryst. A51, 880-887
41. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674
42. McCoy, A. J. & Read, R. J. (2010). Acta Cryst. D66, 458-469
43. Mueller-Dieckmann, C., Panjikar, S., Schmidt, A., Mueller, S., Kuper, J., Geerlof, A., Wilmanns, M., Singh, R. K., Tucker, P. A. & Weiss, M. S. (2007). Acta Cryst. D63, 366-380
44. Müller, P., Köpke, S. & Sheldrick, G. M. (2003). Acta Cryst. D59, 32-37
45. Nayal, M. & Di Cera, E. (1994). Proc. Natl Acad. Sci. USA, 91, 817-821
46. Nayal, M. & Di Cera, E. (1996). J. Mol. Biol. 256, 228-234
47. Pauling, L. (1929). J. Am. Chem. Soc. 51, 1010-1026
48. Read, R. J. (1986). Acta Cryst. A42, 140-149
49. Read, R. J. & McCoy, A. J. (2011). Acta Cryst. D67, 338-344
50. Rimsa, V., Eadsforth, T. & Hunter, W. N. (2011). Acta Cryst. F67, 442-445
51. Roach, J. (2003). Methods Enzymol. 374, 137-145
52. Rulísek, L. & Vondrásek, J. (1998). J. Inorg. Biochem. 71, 115-127
53. Thorn, A. & Sheldrick, G. M. (2011). J. Appl. Cryst. 44, 1285-1287
54. Totir, M., Echols, N., Nanao, M., Gee, C. L., Moskaleva, A., Gradia, S., Iavarone, A. T., Berger, J. M., May, A. P., Zubieta, C. & Alber, T. (2012). PLoS One, 7, e32498
55. Turk, D. (1992). PhD thesis. Technische Universität München, Germany
56. Turk, D. (2013). Acta Cryst. D69, 1342-1357
57. Urzhumtsev, A. G., Skovoroda, T. P. & Lunin, V. Y. (1996). J. Appl. Cryst. 29, 741-744
58. Wilson, M. A. & Brunger, A. T. (2000). J. Mol. Biol. 301, 1237-1256
59. Word, J. M., Lovell, S. C., Richardson, J. S. & Richardson, D. C. (1999). J. Mol. Biol. 285, 1735-1747
60. Xu, Y., Feng, L., Jeffrey, P. D., Shi, Y. & Morel, F. M. (2008). Nature (London), 452, 56-61
61. Zhang, J., Yang, W., Piquemal, J.-P. & Ren, P. (2012). J. Chem. Theory Comput. 8, 1314-1324
62. Zheng, H., Chordia, M. D., Cooper, D. R., Chruszcz, M., Müller, P., Sheldrick, G. M. & Minor, W. (2013). Nature Protoc. 9, 156-170
63. Zheng, H., Chruszcz, M., Lasota, P., Lebioda, L. & Minor, W. (2008). J. Inorg. Biochem. 102, 1765-1776