Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT

Acta Crystallographica Section D: Biological Crystallography

Volumn 60, Issue 12 I, 2004, Pages 2210-2221

  Blanc, E ^a,b   Roversi, P ^a,c   Vonrhein, C ^a   Flensburg, C ^a   Lea, S M ^c   Bricogne, G ^a  

^a GLOBAL PHASING LTD   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DECAY ACCELERATING FACTOR; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; NORMAL DISTRIBUTION; PROTEIN CONFORMATION; STATISTICAL MODEL; STATISTICS; TEMPERATURE; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; ANTIGENS, CD55; CRYSTALLOGRAPHY, X-RAY; LIKELIHOOD FUNCTIONS; MODELS, MOLECULAR; NORMAL DISTRIBUTION; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; TEMPERATURE;

EID: 14844321328     PISSN: 09074449     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0907444904016427     Document Type: Article

References (55)

1. Abrahams, J. P. (1997). Acta Cryst. D53, 371-376.
2. Abrahams, J. P. & Leslie, A. (1996). Acta Cryst. D52, 30-42.
3. Bard, J., Zhelkovsky, A., Helmling, S., Earnest, T., Moore, C. & Bohm, A. (2000). Science, 289, 1346-1349.
4. Benach, J., Filling, C., Oppermann, U., Roversi, P., Bricogne, G., Berndt, K., Jornvall, H. & Ladenstein, R. (2002). Biochemistry, 41, 14659-14668.
5. Bertaut, E. (1955a). Acta Cryst. 8, 537-543.
6. Bertaut, E. (1955b). Acta Cryst. 8, 544-548.
7. Blow, D. M. & Crick, F. H. C. (1959). Acta Cryst. A12, 794-802.
8. Bricogne, G. (1984). Acta Cryst. A40, 410-445.
9. Bricogne, G. (1988). Acta Cryst. A44, 517-545.
10. Bricogne, G. (1993a). Acta Cryst. D49, 37-60.
11. Bricogne, G. (1993b). International Tables for Crystallography, edited by U. Shmueli, Vol. B, pp. 23-106. Dordrecht, Holland: Kluwer Academic Publishers.
12. Bricogne, G. (1997). Methods Enzymol. 276, 424-448.
13. Bricogne, G. & Irwin, J. J. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 85-92. Warrington: Daresbury Laboratory.
14. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
15. Cowtan, K. (2002). J. Appl. Cryst. 35, 655-663.
16. Cowtan, K. & Main, P. (1993). Acta Cryst. D49, 148-157.
17. Delft, F. von, Lewendon, A., Dhanaraj, V., Blundell, T., Abell, C. & Smith, A. (2001). Structure, 9, 439-450.
18. Dessen, A., Tang, J., Schmidt, H., Stahl, M., Clark, J., Seehra, J. & Somers, W. (1999). Cell, 97, 349-360.
19. Fischmann, T., Hruza, A., Niu, X., Fossetta, J., Lunn, C., Dolphin, E., Prongay, A., Reichert, P., Lundell, D., Narula, S. & Weber, P. (1999). Nature Struct. Biol. 6, 233-242.
20. Glykos, N. M. & Kokkinidis, M. (2000). Acta Cryst. D56, 1070-1072.
21. Guo, D., Blessing, R. H. & Langs, D. A. (2000). Acta Cryst. D56, 451-457.
22. Han, M., Gurevich, V., Vishnivetskiy, S., Sigler, P. & Schubert, C. (2001). Structure, 9, 869-880.
23. Hanzal-Bayer, M., Renault, L., Roversi, P., Wittinghofer, A. & Hillig, R. (2002). EMBO J. 21, 2095-2106.
24. Hendrickson, W. & Lattman, E. (1970). Acta Cryst. B26, 136-143.
25. Izard, T., Evans, G., Borgon, R., Rush, C., Bricogne, G. & Bois, P. (2003). Nature (London), 427, 171-175.
26. Jones, E., Walker, N. & Stuart, D. (1991). Acta Cryst. A47, 753-770.
27. Koronakis, V., Sharff, A., Koronakis, E., Luisi, B. & Hughes, C. (2000). Nature (London), 405, 914-919.
28. La Fortelle, E. de & Bricogne, G. (1997). Methods Enzymol. 276, 472-494.
29. Leslie, A. G. W. (1987). Acta Cryst. A43, 134-136.
30. Lukacik, P., Roversi, P., White, J., Esser, D., Smith, G., Billington, J., Williams, P., Rudd, P., Wormald, M., Harvey, D., Crispin, M., Radcliffe, C., Dwek, R., Evans, D., Morgan, B., Smith, R. & Lea, S. (2004). Proc. Natl Acad. Sci. USA, 101, 1279-1284.
31. Luzzati, V. (1952). Acta Cryst. 5, 802-810.
32. McRee, D. (1999). J. Struct. Biol. 125, 156-165.
33. Madison, V. et al. (2002). Biophys. Chem. 101-102, 239-247.
34. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
35. Ng, K. K., Petersen, J. F., Cherney, M. M., Garen, C., Zalatoris, J. J., Rao-Naik, C., Dunn, B. M., Martzen, M. R., Peanasky, R. J. & James, M. N. (2000). Nature Struct. Biol. 7, 653-657.
36. Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J. (1998). Acta Cryst. D54, 1285-1294.
37. Pannu, N. S. & Read, R. J. (1996). Acta Cryst. A52, 659-668.
38. Read, R. J. (1986). Acta Cryst. A42, 140-149.
39. Retailleau, P., Huang, X., Yin, Y., Hu, M., Weinreb, V., Vachette, P., Vonrhein, C., Bricogne, G., Roversi, P., Ilyin, V. & Carter, C. J. (2003). J. Mol. Biol., 325, 39-63.
40. Reynolds, R., Remington, S., Weaver, L., Fisher, R., Anderson, W., Ammon, H. & Matthews, B. (1985). Acta Cryst. B41, 139-147.
41. Roversi, P., Blanc, E., Vonrhein, C., Evans, G. & Bricogne, G. (2000). Acta Cryst. D56, 1316-1323.
42. Roversi, P., Irwin, J. J. & Bricogne, G. (1998). Acta Cryst. A54, 971-996.
43. Sagermann, M. & Matthews, B. (2002). J. Mol. Biol. 316, 931-940.
44. Somers, W., Tang, J., Shaw, G. & Camphausen, R. (2000). Cell, 103, 467-479.
45. Srinivasan, R. (1966). Acta Cryst. 20, 143-144.
46. Svensson, S., Ostberg, T., Jacobsson, M., Norstrom, C., Stefansson, K., Hallen, D., Johansson, I., Zachrisson, K., Ogg, D. & Jendeberg, L. (2003). EMBO J. 22, 4625-4633.
47. Tronrud, D. E. (1992). Acta Cryst. A48, 912-916.
48. Tronrud, D. E. (1996). J. Appl. Cryst. 29, 100-104.
49. Tronrud, D. E. (1997). Methods Enzymol. 277, 306-319.
50. Tronrud, D. E. (1999). Acta Cryst. A55, 700-703.
51. Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). Acta Cryst. A43, 489-501.
52. Vagin, A. & Teplyakov, A. (2000). Acta Cryst. D56, 1622-1624.
53. Vicens, Q. & Westhof, E. (2002). Chem. Biol. 9, 747-755.
54. Wang, B.-C. (1985). Methods Enzymol. 12, 813-815.
55. Williams, P., Chaudhry, Y., Goodfellow, I., Billington, J., Powell, R., Spiller, O., Evans, D. & Lea, S. (2003). Proc. Natl Acad. Sci. USA, 278, 10691-10696.