Averaged kick maps: Less noise, more signal and probably less bias

Acta Crystallographica Section D: Biological Crystallography

Volumn 65, Issue 9, 2009, Pages 921-931

  Pražnikar, Jure ^a   Afonine, Pavel V ^b   Gunčar, Gregor ^a   Adams, Paul D ^b,c   Turk, Dušan ^a  

^a JO EF STEFAN INSTITUTE   (Slovenia)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c University of California at Berkeley   (United States)

Author keywords

Density map calculation; Kick maps; Maximum likelihood; Model bias; OMIT maps

Indexed keywords

ARTICLE; COMPUTER PROGRAM; STATISTICAL MODEL; THEORETICAL MODEL; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; LIKELIHOOD FUNCTIONS; MODELS, THEORETICAL; SOFTWARE;

EID: 69949128280     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444909021933     Document Type: Article

References (63)

1. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K. & Terwilliger, T. C. (2002). Acta Cryst. D58, 1948-1954.
2. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005a). CCP4 Newsl. 42, contribution 8.
3. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005b). Acta Cryst. D61, 850-855.
4. Badger, J. (1997). Methods Enzymol. 277, 344-352.
5. Baker, E. N. (1980). J. Mol. Biol. 141, 441-484.
6. Bhat, T. N. (1988). J. Appl. Cryst. 21, 279-281.
7. Bhat, T. N. & Cohen, G. H. (1984). J. Appl. Cryst. 17, 244-248.
8. Brünger, A. T. (1992). Nature (London), 355, 472-474.
9. Brunger, A. T. (2007). Nature Protoc. 2, 2728-2733.
10. Brünger, A. T., Adams, P. D. & Rice, L. M. (1998). Direct Methods for Solving Macromolecular Structures, edited by S. Fortier, pp. 143-157. Dordrecht: Kluwer Academic Publishers.
11. Cai, Y., Cronin, C. N., Engel, A. G., Ohno, K., Hersh, L. B. & Rodgers, D. W. (2004). EMBO J. 23, 2047-2058.
12. Cooper, S. J., Leonard, G. A., McSweeney, S. M., Thompson, A. W., Naismith, J. H., Qamar, S., Plater, A., Berry, A. & Hunter, W. N. (1996). Structure, 4, 1303-1315.
13. Fernandez-Catalan, C., Bode, W., Huber, R., Turk, D., Calvete, J. J., Lichte, A., Tschesche, H. & Maskos, K. (1998). EMBO J. 17, 5238-5248.
14. Fokine, A. & Urzhumtsev, A. (2002). Acta Cryst. D58, 1387-1392.
15. Gunčar, G., Podobnik, M., Pungerčar, J.,Štrukelj, B., Turk, V. & Turk, D. (1998). Structure, 6, 51-61.
16. Gunčar, G., Klemenčič, I., Turk, B., Turk, V., Karaoglanovic Carmona, A., Juliano, L. & Turk, D. (2000). Structure, 8, 305-313.
17. Hall, D. R., Leonard, G. A., Reed, C. D., Watt, C. I., Berry, A. & Hunter, W. N. (1999). J. Mol. Biol. 287, 383-394.
18. Hodel, A., Kim, S.-H. & Brünger, A. T. (1992). Acta Cryst. A48, 851-858.
19. Jenko, K. S., Gunčar, G., Štern, I., Morgan, G., Rabzelj, S., Kenig, M., Staniforth, R. A., Waltho, J. P., Žerovnik, E. & Turk, D. (2007). J. Mol. Biol. 366, 1569-1579.
20. Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100-115.
21. Keith, C., Feldman, D. S., Deganello, S., Glick, J., Ward, K. B., Jones, E. O. & Sigler, P. B. (1981). J. Biol. Chem. 256, 8602-8607.
22. Kim, A. R., Rylett, R. J. & Shilton, B. H. (2006). Biochemistry, 45, 14621-14631.
23. Kissinger, C. R., Gehlhaar, D. K. & Fogel, D. B. (1999). Acta Cryst. D55, 484-491.
24. Kleywegt, G. J., Harris, M. R., Zou, J., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). Acta Cryst. D60, 2240-2249.
25. Ko, T.-P., Day, J., Greenwood, A. & McPherson, A. (1994). Acta Cryst. D50, 813-825.
26. Liu, B., Bartlam, M., Gao, R., Zhou, W., Pang, H., Liu, Y., Feng, Y. & Rao, Z. (2004). Biophys. J. 86, 420-427.
27. Lunin, V. Yu. & Woolfson, M. M. (1993). Acta Cryst. D49, 530-533.
28. Lunin, V. Yu. & Skovoroda, T. P. (1995). Acta Cryst. A51, 880-887.
29. Luzzati, V. (1953). Acta Cryst. 6, 142-152.
30. Main, P. (1979). Acta Cryst. A35, 779-785.
31. Moews, P. C. & Kretsinger, R. H. (1975). J. Mol. Biol. 91, 201-228.
32. Murshudov, G. N., Davies, G. J., Isupov, M., Krzywda, S. & Dodson, E. J. (1998). CCP4 Newsl. 35, 37-43.
33. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
34. Pannu, N. S. & Read, R. J. (1996). Acta Cryst. A52, 659-668.
35. Perrakis, A., Sixma, T. K., Wilson, K. S. & Lamzin, V. S. (1997). Acta Cryst. D53, 448-455.
36. Phillips, S. E. V. (1980). J. Mol. Biol. 142, 531-554.
37. Ramachandran, G. N. & Raman, S. (1959). Acta Cryst. 12, 957-964.
38. Ramachandran, G. N. & Srinivasan, R. (1961). Nature (London), 190, 159-161.
39. Ramachandran, G. N. & Srinivasan, R. (1970). Fourier Methods in Crystallography. New York: Wiley.
40. Raman, S. (1959). Acta Cryst. 12, 964-975.
41. Read, R. J. (1986). Acta Cryst. A42, 140-149.
42. Rice, L. M., Shamoo, Y. & Brünger, A. T. (1998). J. Appl. Cryst. 31, 798-805.
43. Rossmann, M. G. (1972). The Molecular Replacement Method. New York: Gordon & Breach.
44. Rossmann, M. G. & Blow, D. M. (1963). Acta Cryst. 16, 39-45.
45. Sheriff, S. & Hendrickson, W. A. (1987). Acta Cryst. A43, 118-121.
46. Sim, G. A. (1959). Acta Cryst. 12, 813-815.
47. Srinivasan, R. (1961). Proc. Indian Acad. Sci. A, 53, 252-264.
48. Terwilliger, T. C. (2004). Acta Cryst. D60, 2144-2149.
49. 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.
50. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N.W., Adams, P. D., Read, R. J., Zwart, P. H. & Hung, L.-W. (2008). Acta Cryst. D64, 515-524.
51. Than, M. E., Bourenkov, G. P., Henrich, S., Mann, K. & Bode, W. (2005). Biol. Chem. 386, 759-766.
52. Than, M. E., Henrich, S., Huber, R., Ries, A., Mann, K., Kühn, K., Timpl, R., Bourenkov, G. P., Bartunik, H. D. & Bode, W. (2002). Proc. Natl Acad. Sci. USA, 99, 6607-6612.
53. Tronrud, D. E. (1997). Methods Enzymol. 277, 306-319.
54. Turk, D. (1992). PhD thesis. Technische Universität, München, Germany.
55. Turk, D. (1997). ACA Meeting Abstracts, 24, 76.
56. Turk, D. (2007). Evolving Methods for Macromolecular Crystallography, edited by R. J. Read & J. L. Sussman, pp. 111-122. New York: Springer.
57. Turk, D., Podobnik, M., Kuhelj, R., Dolinar, M. & Turk, V. (1996). FEBS Lett. 384, 211-214.
58. Urzhumtsev, A. G. (2000). CCP4 Newsl. 38, 38-49.
59. Urzhumtsev, A. G., Skovoroda, T. P. & Lunin, V. Y. (1996). J. Appl. Cryst. 29, 741-744.
60. Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H. J. & Sheldrick, G. M. (1999). Acta Cryst. D55, 1158-1167.
61. Vijayan, M. (1980). Acta Cryst. A36, 295-298.
62. Watenpaugh, K. D., Sieker, L. C., Herriott, J. R. & Jensen, L. H. (1973). Acta Cryst. B29, 943-956.
63. Woolfson, M. M. (1956). Acta Cryst. 9, 804-810.