Polarizable atomic multipole X-ray refinement: Weighting schemes for macromolecular diffraction

Acta Crystallographica Section D: Biological Crystallography

Volumn 67, Issue 11, 2011, Pages 957-965

  Fenn, T D ^a   Schnieders, M J ^b  

^a Stanford University   (United States)

^b The University of Texas at Austin   (United States)

Author keywords

refinement; weighting

Indexed keywords

PROTEIN;

ANIMAL; ARTICLE; BIOLOGY; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; CRYSTALLIZATION; HUMAN; MACROMOLECULE; MOLECULAR WEIGHT; PROTEIN CONFORMATION; STATISTICAL MODEL; THEORETICAL MODEL; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ANIMALS; COMPUTATIONAL BIOLOGY; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; HUMANS; LIKELIHOOD FUNCTIONS; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MODELS, THEORETICAL; MOLECULAR WEIGHT; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; X-RAY DIFFRACTION;

EID: 80955139670     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444911039060     Document Type: Article

References (57)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Proc. Natl. Acad. Sci. USA, 94, 5018-5023.
3. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005a). CCP4 Newsl. Protein Crystallogr. 42, 43-49.
4. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005b). Acta Cryst. D61, 850-855.
5. Arendall, W. B. III, Tempel, W., Richardson, J. S., Zhou, W., Wang, S., Davis, I. W., Liu, Z.-J., Rose, J. P., Carson, W. M., Luo, M., Richardson, D. C. & Wang, B.-C. (2005). J. Struct. Funct. Genomics, 6, 1-11.
6. Baker, E. N. & Hubbard, R. E. (1984). Prog. Biophys. Mol. Biol. 44, 97-179.
7. Berkholz, D. S., Shapovalov, M. V., Dunbrack, R. L. & Karplus, P. A. (2009). Structure, 17, 1316-1325.
8. Bhattacharya, A., Tejero, R. & Montelione, G. T. (2007). Proteins, 66, 778-795.
9. Bricogne, G. (2006). International Tables for Crystallography, Vol. B, Reciprocal Space, 1st online ed., edited by U. Shmueli, pp. 25-98. Chester: International Union of Crystallography.
10. Brünger, A. T. (1988). J. Mol. Biol. 203, 803-816.
11. Brünger, A. T. (1989). Acta Cryst. A45, 42-50.
12. Brünger, A. T. (1992). Nature (London), 355, 472-475.
13. 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.
14. Cowtan, K. (2002). J. Appl. Cryst. 35, 655-663.
15. Cowtan, K. (2005). J. Appl. Cryst. 38, 193-198.
16. Darden, T., York, D. & Pedersen, L. (1993). J. Chem. Phys. 98, 10089-10092.
17. Echols, N., Headd, J. J., Afonine, P. & Adams, P. D. (2010). Comput. Crystallogr. Newsl. 1, 12-17.
18. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
19. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H. & Pedersen, L. G. (1995). J. Chem. Phys. 103, 8577-8593.
20. Fabiola, F., Bertram, R., Korostelev, A. & Chapman, M. S. (2002). Protein Sci. 11, 1415-1423.
21. Fabiola, G. F., Krishnaswamy, S., Nagarajan, V. & Pattabhi, V. (1997). Acta Cryst. D53, 316-320.
22. Faver, J. C., Benson, M. L., He, X., Roberts, B. P., Wang, B., Marshall, M. S., Sherrill, C. D. & Merz, K. M. Jr (2011). PLoS One, 6, e18868.
23. Fenn, T. D., Schnieders, M. J. & Brunger, A. T. (2010). Acta Cryst. D66, 1024-1031.
24. Fenn, T. D., Schnieders, M. J., Brunger, A. T. & Pande, V. S. (2010). Biophys. J. 98, 2984-2992.
25. Fenn, T. D., Schnieders, M. J., Mustyakimov, M., Wu, C., Langan, P., Pande, V. S. & Brunger, A. T. (2011). Structure, 19, 523-533.
26. Ford, G. C. & Rollett, J. S. (1970). Acta Cryst. A26, 162.
27. Habeck, M., Rieping, W. & Nilges, M. (2006). Proc. Natl. Acad. Sci. USA, 103, 1756-1761.
28. Ho, B. K. & Curmi, M. G. (2002). J. Mol. Biol. 317, 291-308.
29. Jack, A. & Levitt, M. (1978). Acta Cryst. A34, 931-935.
30. Jiao, D., Golubkov, P. A., Darden, T. A. & Ren, P. (2008). Proc. Natl. Acad. Sci. USA, 105, 6290-6295.
31. Jorgensen, W. L. & Tirado-Rives, J. (1988). J. Am. Chem. Soc. 110, 1657-1666.
32. Lebedev, A. A., Tickle, I. J., Laskowski, R. A. & Moss, D. S. (2003). Acta Cryst. D59, 1557-1566.
33. Linge, J. P., Williams, M. A., Spronk, C. A., Bonvin, A. M. & Nilges, M. (2003). Proteins, 50, 496-506.
34. Lopes, P. E., Roux, B. & Mackerell, A. D. (2009). Theor. Chem. Acc. 124, 11-28.
35. McCoy, A. J. (2004). Acta Cryst. D60, 2169-2183.
36. Morozov, A. V., Kortemme, T., Tsemekhman, K. & Baker, D. (2004). Proc. Natl. Acad. Sci. USA, 101, 6946-6951.
37. 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.
38. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
39. Nozinovic, S., Fürtig, B., Jonker, H. R., Richter, C. & Schwalbe, H. (2010). Nucleic Acids Res. 38, 683-694.
40. Panigrahi, S. K. & Desiraju, G. R. (2007). J. Biosci. 32, 677-691.
41. Ponder, J. W. & Case, D. A. (2003). Adv. Protein Chem. 66, 27-85.
42. Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., Head-Gordon, M., Clark, G. N., Johnson, M. E. & Head-Gordon, T. (2010). J. Phys. Chem. B, 114, 2549-2564.
43. Read, R. J. (2010). Structure, 18, 664-665.
44. Ren, P. & Ponder, J. W. (2003). J. Phys. Chem. B, 107, 5933-5947.
45. Ren, P. & Ponder, J. W. (2004). J. Phys. Chem. B, 108, 13427-13437.
46. Ren, P., Wu, C. & Ponder, J. W. (2011). J. Chem. Theor. Comput., doi:10.1021/ct200304d.
47. Sagui, C., Pedersen, L. G. & Darden, T. A. (2004). J. Chem. Phys. 120, 73-87.
48. Schnieders, M. J., Fenn, T. D. & Pande, V. S. (2011). J. Chem. Theor. Comput. 7, 1141-1156.
49. Schnieders, M. J., Fenn, T. D., Pande, V. S. & Brunger, A. T. (2009). Acta Cryst. D65, 952-965.
50. Schröder, G. F., Levitt, M. & Brunger, A. T. (2010). Nature (London), 464, 1218-1222.
51. Ten Eyck, L. F. (1973). Acta Cryst. A29, 183-191.
52. Ten Eyck, L. F. (1977). Acta Cryst. A33, 486-492.
53. Touw, W. G. & Vriend, G. (2010). Acta Cryst. D66, 1341-1350.
54. Tronrud, D. E., Berkholz, D. S. & Karplus, P. A. (2010). Acta Cryst. D66, 834-842.
55. Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N. (2004). Acta Cryst. D60, 2184-2195.
56. Wang, H. & Stubbs, G. (1993). Acta Cryst. A49, 504-513.
57. Waser, J. (1955). Acta Cryst. 8, 595.