Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Acta Crystallographica Section D: Biological Crystallography

Volumn 68, Issue 4, 2012, Pages 381-390

  Headd, Jeffrey J ^a   Echols, Nathaniel ^a   Afonine, Pavel V ^a   Grosse Kunstleve, Ralf W ^a   Chen, Vincent B ^b   Moriarty, Nigel W ^a   Richardson, David C ^b   Richardson, Jane S ^b   Adams, Paul D ^a,c  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b DUKE UNIVERSITY   (United States)

^c University of California at Berkeley   (United States)

Author keywords

automation Model building, refinement and validation; low resolution; macromolecular crystallography; refinement

Indexed keywords

DNA; PROTEIN;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; METHODOLOGY; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; CRYSTALLOGRAPHY, X-RAY; DNA; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE;

EID: 84860279341     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444911047834     Document Type: Article

References (48)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Afonine, P., Grosse-Kunstleve, R. & Adams, P. (2005). CCP4 Newsl. Protein Crystallogr. 42, contribution 8.
3. Berman, H., Henrick, K. & Nakamura, H. (2003). Nature Struct. Biol. 10, 980.
4. Bradley, P., Misura, K. M. & Baker, D. (2005). Science, 309, 1868-1871.
5. Bricogne, G., Blanc, E., Brandl,M., Flensburg, C., Keller, P., Paciorek, W., Roversi, P., Sharff, A., Smart, O. & Vonrhein, C. (2010). BUSTER. Cambridge: Global Phasing Ltd.
6. Brünger, A. T. 1992a). X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. New Haven: Yale University Press.
7. Brünger, A. T. 1992b Nature (London) 355 472-475.
8. Brunger, A. T. (2007). Nature Protoc. 2, 2728-2733.
9. 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.
10. Chen, V. B. (2010). PhD thesis, Duke University, USA.
11. 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.
12. Chen, V. B., Davis, I. W. & Richardson, D. C. (2009). Protein Sci. 18, 2403-2409.
13. Dennis, J. E. Jr & Welsch, R. E. (1978). Commun. Stat. Simul. Comput. 7, 345-359.
14. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
15. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
16. Fabiola, F., Bertram, R., Korostelev, A. & Chapman, M. S. (2002). Protein Sci. 11, 1415-1423.
17. Geman, S. A. & McClure, D. E. (1987). Bull Int. Stat. Inst. 52, 5-21.
18. Headd, J. J. (2009). PhD thesis, Duke University, USA.
19. Headd, J. J., Immormino, R.M., Keedy, D. A., Emsley, P., Richardson, D. C. & Richardson, J. S. (2009). J. Struct. Funct. Genomics, 10, 83-93.
20. Hintze, B. J. & Johnson, S. J. (2010). J. Appl. Cryst. 43, 1540-1542.
21. Kabsch, W. & Sander, C. (1983). Biopolymers, 22, 2577-2637.
22. Karmali, A. M., Blundell, T. L. & Furnham, N. (2009). Acta Cryst. D65, 121-127.
23. Kim, J. J., Casteel, D. E., Huang, G., Kwon, T. H., Ren, R. K., Zwart, P., Headd, J. J., Brown, N. G., Chow, D.-C., Palzkill, T. & Kim, C. (2011). PLoS One, 6, e18413.
24. Kleywegt, G. J. & Brünger, A. T. (1996). Structure, 4, 897-904.
25. Kleywegt, G. J. & Jones, T. A. (1996). Structure, 4, 1395-1400.
26. Kleywegt, G. J. & Jones, T. A. (1997). Methods Enzymol. 277, 208-230.
27. Kleywegt, G. J. & Jones, T. A. (1998). Acta Cryst. D54, 1119-1131.
28. Koparde, V. N., Scarsdale, J. N. & Kellogg, G. E. (2011). PLoS One, 6, e15920.
29. Leontis, N. B. & Westhof, E. (2001). RNA, 7, 499-512.
30. Lovell, S. C., Davis, I. W., Arendall, W. B. III, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S. & Richardson, D. C. (2003). Proteins, 50, 437-450.
31. Lovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. (2000). Proteins, 40, 389-408.
32. 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.
33. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
34. Oldfield, T. J. (2001). Acta Cryst. D57, 82-94.
35. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). J. Comput. Chem. 25, 1605-1612.
36. Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag.
37. Schröder, G. F., Levitt, M. & Brunger, A. T. (2010). Nature (London), 464, 1218-1222.
38. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
39. Smart, O., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Vonrhein, C., Womack, T. & Bricogne, G. (2008). Abstr. Annu. Meet. Am. Crystallogr. Assoc., Abstract TP139, p. 117.
40. Storici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. & Schirmer, T. (2004). J. Biol. Chem. 279, 363-373.
41. Sussman, J. L., Holbrook, S. R., Church, G. M. & Kim, S.-H. (1977). Acta Cryst. A33, 800-804.
42. Tronrud, D. E., Berkholz, D. S. & Karplus, P. A. (2010). Acta Cryst. D66, 834-842.
43. Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). Acta Cryst. A43, 489-501.
44. Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H. J. & Sheldrick, G. M. (1999). Acta Cryst. D55, 1158-1167.
45. Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N. (2004). Acta Cryst. D60, 2184-2195.
46. Word, J. M., Bateman, R. C., Presley, B. K., Lovell, S. C. & Richardson, D. C. 2000 Protein Sci. 9 2251-2259.
47. 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.
48. Word, J. M., Lovell, S. C., Richardson, J. S. & Richardson, D. C. 1999). J. Mol. Biol. 285 1735-1747.