Percentile-based spread: A more accurate way to compare crystallographic models

Acta Crystallographica Section D: Biological Crystallography

Volumn 66, Issue 9, 2010, Pages 970-978

  Pozharski, Edwin ^a  

^a UNIVERSITY OF MARYLAND   (United States)

Author keywords

model precision; r.m.s.d.; structural comparison

Indexed keywords

ANTIBODY; COCAINE; MORPHINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; IMMUNOLOGY; METHODOLOGY; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY; PROCEDURES;

ANTIBODIES; COCAINE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MORPHINE; PROTEIN STRUCTURE, TERTIARY;

EID: 77956551236     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444910027927     Document Type: Article

References (35)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Artymiuk, P. J., Blake, C. C. F., Rice, D. W. & Wilson, K. S. (1982). Acta Cryst. B38, 778-783.
3. Bedem, H. van den, Dhanik, A., Latombe, J.-C. & Deacon, A. M. (2009). Acta Cryst. D65, 1107-1117.
4. Blow, D. M. (2002). Acta Cryst. D58, 792-797.
5. Chambers, J. L. & Stroud, R. M. (1979). Acta Cryst. B35, 1861-1874.
6. Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
7. DePristo, M. A., de Bakker, P. I. W. & Blundell, T. L. (2004). Structure, 12, 831-838.
8. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
9. Ettmayer, P., France, D., Gounarides, J., Jarosinski, M., Martin, M.-S., Rondeau, J.-M., Sabio, M., Topiol, S., Weidmann, B., Zurini, M. & Bair, K. W. (1999). J. Med. Chem. 42, 971-980.
10. Furnham, N., Blundell, T. L., DePristo, M. A. & Terwilliger, T. C. (2006). Nature Struct. Mol. Biol. 13, 184-185.
11. Gill, H. S., Pfluegl, G. M. U. & Eisenberg, D. (2002). Biochemistry, 41, 9863-9872.
12. Greasley, S. E., Yamashita, M. M., Cai, H., Benkovic, S. J., Boger, D. L. & Wilson, I. A. (1999). Biochemistry, 38, 16783-16793.
13. Kabsch, W. (1976). Acta Cryst. A32, 922-923.
14. Kallen, J.,Welzenbach, K., Ramage, P., Geyl, D., Kriwacki, R., Legge, G., Cottens, S., Weitz-Schmidt, G. & Hommel, U. (1999). J. Mol. Biol. 292, 1-9.
15. Levin, E. J., Kondrashov, D. A., Wesenberg, G. E. & Phillips, G. N. (2007). Structure, 15, 1040-1052.
16. Murshudov, G. N. & Dodson, E. J. (1997). CCP4 Newsl. 33, 31-39.
17. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
18. Pellegrini, M., Grønbech-Jensen, N., Kelly, J. A., Pfluegl, G. M. U. & Yeates, T. O. (1997). Proteins, 29, 426-432.
19. Pozharski, E., Moulin, A., Hewagama, A., Shanafelt, A. B., Petsko, G. A. & Ringe, D. (2005). J. Mol. Biol. 349, 570-582.
20. Pozharski, E.,Wilson, M. A., Hewagama, A., Shanafelt, A. B., Petsko, G. & Ringe, D. (2004). J. Mol. Biol. 337, 691-697.
21. Rashin, A. A., Rashin, A. H. L. & Jernigan, R. L. (2009). Acta Cryst. D65, 1140-1161.
22. Roszak, A. W., McKendrick, K., Gardiner, A. T., Mitchell, I. A., Isaacs, N. W., Cogdell, R. J., Hashimoto, H. & Frank, H. A. (2004). Structure, 12, 765-773.
23. Saijo, S., Yamada, Y., Sato, T., Tanaka, N., Matsui, T., Sazaki, G., Nakajima, K. & Matsuura, Y. (2005). Acta Cryst. D61, 207-217.
24. Schrøder, H. K., Willassen, N. P. & Smalås, A. O. (1998). Acta Cryst. D54, 780-798.
25. Schwarzenbacher, R., Zeth, K., Diederichs, K., Gries, A., Kostner, G. M., Laggner, P. & Prassl, R. (1999). EMBO J. 18, 6228-6239.
26. Takafumi, U., Satoshi, A., Tomomi, K., Takahiro, O., Tatsuo, H. & Yoshihito, W. (2010). Chem. Eur. J. 16, 2730-2740.
27. Tame, J. R. H. & Vallone, B. (2000). Acta Cryst. D56, 805-811.
28. 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.
29. Vandeputte-Rutten, L., Bos, M. P., Tommassen, J. & Gros, P. (2003). J. Biol. Chem. 278, 24825-24830.
30. Vaney, M. C., Broutin, I., Retailleau, P., Douangamath, A., Lafont, S., Hamiaux, C., Prangé, T., Ducruix, A. & Riès-Kautt, M. (2001). Acta Cryst. D57, 929-940.
31. Vaney, M. C., Maignan, S., Riès-Kautt, M. & Ducruix, A. (1996). Acta Cryst. D52, 505-517.
32. Vitkup, D., Ringe, D., Karplus, M. & Petsko, G. A. (2002). Proteins, 46, 345-354.
33. Walsh, M. A., Schneider, T. R., Sieker, L. C., Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1998). Acta Cryst. D54, 522-546.
34. Williams, P. A., Fü löp, V., Garman, E. F., Saunders, N. F.W., Ferguson, S. J. & Hajdu, J. (1997). Nature (London), 389, 406-412.
35. Wright, L. et al. (2004). Chem. Biol. 11, 775-785.