Validation of protein crystal structures

Acta Crystallographica Section D: Biological Crystallography

Volumn 56, Issue 3, 2000, Pages 249-265

  Kleywegt, Gerard J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CHEMICAL STRUCTURE; EDUCATION; EVALUATION; HUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OBSERVER VARIATION; PROTEIN CONFORMATION; REVIEW; X RAY CRYSTALLOGRAPHY;

BIOCHEMISTRY; CRYSTALLOGRAPHY, X-RAY; EVALUATION STUDIES; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; OBSERVER VARIATION; PROTEIN CONFORMATION;

EID: 0034013435     PISSN: 09074449     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0907444999016364     Document Type: Review

References (139)

1. Aalten, D. M. F. van, Bywater, R., Findlay, J. B. C., Hendlich, M., Hooft, R. W. W. & Vriend, G. (1996). J. Comput. Aided Mol. Des. 10, 255-262.
2. Abagyan, R. A. & Totrov, M. M. (1997). J. Mol. Biol. 268, 678-685.
3. Abola, E. E., Bairoch, A., Barker, W. C., Beck, S., Benson, D. A., Berman, H., Cantor, C., Doubet, S., Hubbard, T. J. P., Jones, T. A., Kleywegt, G. J., Kolaskar, A. S., van Kuik, A., Lesk, A. M., Mewes, H. W., Neuhaus, D., Pfeiffer, F., Ten Eyck, L. F., Simpson, R. J., Stoesser, G., Sussman, J. L., Tateno, Y., Tsugita, A., Ulrich, E. L. & Vliegenthart, J. F. G. (2000). Submitted.
4. Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Proc. Natl Acad. Sci. USA, 94, 5018-5023.
5. Akker, F. van den & Hol, W. G. J. (1999). Acta Cryst. D55, 206-218.
6. Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). Acta Cryst. B35, 2331-2339.
7. Allen, F. H. & Johnson, O. (1991). Acta Cryst. B47, 62-67.
8. Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. II, pp. S1-S19.
9. Ammon, H. L., Weber, I. T., Wlodawer, A., Harrison, R. W., Gilliland, G. L., Murphy, K. C., Sjölin, L. & Roberts, J. (1988). J. Biol. Chem. 263, 150-156.
10. Bacchi, A., Lamzin, V. S. & Wilson, K. S. (1996). Acta Cryst. D52, 641-646.
11. Balasubramanian, R. (1977). Nature (London), 266, 856-857.
12. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). J. Mol. Biol. 112, 535-542.
13. Bhat, T. N. (1988). J. Appl. Cryst. 21, 279-281.
14. Bhat, T. N. & Cohen, G. H. (1984). J. Appl. Cryst. 17, 244-248.
15. Borgstahl, G. E. O., Williams, D. R. & Getzoff, E. D. (1995). Biochemistry, 34, 6278-6287.
16. Bott, R. & Sarma, R. (1976). J. Mol. Biol. 106, 1037-1046.
17. Bowie, J. U., Lüthy, R. & Eisenberg, D. (1991). Science, 253, 164-170.
18. Brändén, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
19. Bricogne, G. & Irwin, 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.
20. Brünger, A. T. (1992a). Nature (London), 355, 472-475.
21. Brünger, A. T. (1992b). X-PLOR. A System for Crystallography and NMR. Yale University, New Haven, Connecticut, USA.
22. Brünger, A. T. (1993). Acta Cryst. D49, 24-36.
23. Brünger, A. T. (1997). Methods Enzymol. 277, 366-396.
24. Carson, M., Buckner, T. W., Yang, Z., Narayana, S. V. L. & Bugg, C. E. (1994). Acta Cryst. D50, 900-909.
25. Carugo, O. & Bordo, D. (1999). Acta Cryst. D55, 479-483.
26. Chapman, M. S. (1995). Acta Cryst. A51, 69-80.
27. Colovos, C. & Yeates, T. O. (1993). Protein Sci. 2, 1511-1519.
28. Cruickshank, D. W. J. (1949). Acta Cryst. 2, 65-82.
29. Cruickshank, D. W. J. (1950). Acta Cryst. 3, 10-13.
30. Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
31. Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275.
32. Divne, C., Ståhlberg, J., Reinikainen, T., Ruohonen, L., Pettersson, G., Knowles, J. K. C., Teeri, T. T. & Jones, T. A. (1994). Science, 265, 524-528.
33. Dodson, E., Kleywegt, G. J. & Wilson, K. S. (1996). Acta Cryst. D52, 228-234.
34. Drenth, J. (1994). Principles of Protein X-ray Crystallography. New York: Springer-Verlag.
35. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
36. EU 3-D Validation Network (1998). J. Mol. Biol. 276, 417-436.
37. Flocco, M. M. & Mowbray, S. L. (1995). Protein Sci. 4, 2118-2122.
38. Greaves, R. B., Vagin, A. A. & Dodson, E. J. (1999). Acta Cryst. D55, 1335-1339.
39. Gunasekaran, K., Ramakrishnan, C. & Balaram, P. (1996). J. Mol. Biol. 264, 191-198.
40. Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
41. Hendrickson, W. A. (1985). Methods Enzymol. 115, 252-270.
42. Hendrickson, W. A. & Konnert, J. H. (1980). Computing in Crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 13.01-13.25. Bangalore: Indian Academy of Science.
43. Herzberg, O. & Moult, J. (1991). Proteins Struct. Funct. Genet. 11, 223-229.
44. Hodel, A., Kim, S.-H. & Brünger, A. T. (1992). Acta Cryst. A48, 851-858.
45. Hoier, H., Schlömann, M., Hammer, A., Glusker, J. P., Carrell, H. L., Goldman, A., Stezowski, J. J. & Heinemann, U. (1994). Acta Cryst. D50, 75-84.
46. Hooft, R. W. W., Sander, C. & Vriend, G. (1994). J. Appl. Cryst. 27, 1006-1009.
47. Hooft, R. W. W., Sander, C. & Vriend, G. (1996a). J. Appl. Cryst. 29, 714-716.
48. Hooft, R. W. W., Sander, C. & Vriend, G. (1996b). Proteins Struct. Funct. Genet. 26, 363-376.
49. Hooft, R. W. W., Sander, C. & Vriend, G. (1997). Comput. Appl. Biosci. 13, 425-430.
50. Hooft, R. W. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Nature (London), 381, 272.
51. IUPAC-IUB Commission on Biochemical Nomenclature (1970). J. Mol. Biol. 52, 1-17.
52. James, M. N. G. & Sielecki, A. R. (1983). J. Mol. Biol. 163, 299-361.
53. Janin, J. (1990). Biochimie, 72, 705-709.
54. Janin, J., Wodak, S., Levitt, M. & Maigret, B. (1978). J. Mol. Biol. 125, 357-386.
55. Jones, T. A. & Kjeldgaard, M. (1994). Proceedings of the CCP4 Study Weekend: From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. A. Waller, pp. 1-13. Warrington: Daresbury Laboratory.
56. Jones, T. A. & Kjeldgaard, M. (1997). Methods Enzymol. 277, 173-208.
57. Jones, T. A., Kleywegt, G. J. & Brünger, A. T. (1996). Nature (London), 381, 18-19.
58. Jones, T. A. & Thirup, S. (1986). EMBO J. 5, 819-822.
59. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
60. Karplus, P. A. (1996). Protein Sci. 5, 1406-1420.
61. Keller, P. A., Henrick, K., McNeil, P., Moodie, S. & Barton, G. J. (1998). Acta Cryst. D54, 1105-1108.
62. Kelly, J. A., Dideberg, O., Charlier, P., Wery, J. P., Libert, M., Moews, P. C., Knox, J. R., Duez, C., Fraipoint, C., Joris, B., Dusart, J., Frère, J. M. & Ghuysen, J. M. (1986). Science, 231, 1429-1431.
63. Kelly, J. A. & Kuzin, A. P. (1995). J. Mol. Biol. 254, 223-236.
64. Kleywegt, G. J. (1996). Acta Cryst. D52, 842-857.
65. Kleywegt, G. J. (1997). J. Mol. Biol. 273, 371-376.
66. Kleywegt, G. J. (1999). Acta Cryst. D55, 1878-1884.
67. Kleywegt, G. J. (2000). International Tables for Crystallography, Vol. F, edited by M. G. Rossmann & E. Arnold, ch. 21.1. Dordrecht: Kluwer Academic Publishers. In the press.
68. Kleywegt, G. J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K. & Jones, T. A. (1994). Structure, 2, 1241-1258.
69. Kleywegt, G. J. & Brünger, A. T. (1996). Structure, 4, 897-904.
70. Kleywegt, G. J., Hoier, H. & Jones, T. A. (1996). Acta Cryst. D52, 858-863.
71. Kleywegt, G. J. & Jones, T. A. (1995a). Proceedings of the CCP4 Study Weekend. Making the Most of Your Model, edited by W. N. Hunter, J. M. Thornton & S. Bailey, pp. 11-24. Warrington: Daresbury Laboratory.
72. Kleywegt, G. J. & Jones, T. A. (1995b). Structure, 3, 535-540.
73. Kleywegt, G. J. & Jones, T. A. (1996a). Acta Cryst. D52, 829-832.
74. Kleywegt, G. J. & Jones, T. A. (1996b). Structure, 4, 1395-1400.
75. Kleywegt, G. J. & Jones, T. A. (1997). Methods Enzymol. 277, 208-230.
76. Kleywegt, G. J. & Jones, T. A. (1998). Acta Cryst. D54, 1119-1131.
77. Kleywegt, G. J. & Read, R. J. (1997). Structure, 5, 1557-1569.
78. Kleywegt, G. J., Zou, J. Y., Divne, C., Davies, G. J., Sinning, I., Ståhlberg, J., Reinikainen, T., Srisodsuk, M., Teeri, T. T. & Jones, T. A. (1997). J. Mol. Biol. 272, 383-397.
79. Korn, A. P. & Rose, D. R. (1994). Protein Eng. 7, 961-967.
80. Kuriyan, J. & Weis, W. I. (1991). Proc. Natl. Acad. Sci. USA, 88, 2773-2777.
81. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
82. Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. (1994). Proceedings of the CCP4 Study Weekend. From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. A. Waller, pp. 149-159. Warrington: Daresbury Laboratory.
83. Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. (1998). Curr. Opin. Struct. Biol. 8, 631-639.
84. Laskowski, R. A., Moss, D. S. & Thornton, J. M. (1993). J. Mol. Biol. 231, 1049-1067.
85. Lubkowski, J., Wlodawer, A., Housset, D., Weber, I. T., Ammon, H. L., Murphy, K. C. & Swain, A. L. (1994). Acta Cryst. D50, 826-832.
86. Lüthy, R., Bowie, J. U. & Eisenberg, D. (1992). Nature (London), 356, 83-85.
87. Luzzati, V. (1952). Acta Cryst. 5, 802-810.
88. MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). Curr. Opin. Struct. Biol. 4, 731-737.
89. MacArthur, M. W. & Thornton, J. M. (1996). J. Mol. Biol. 264, 1180-1195.
90. MacArthur, M. W. & Thornton, J. M. (1999). Acta Cryst. D55, 994-1004.
91. McDonald, I. K. & Thornton, J. M. (1995). Protein Eng. 8, 217-224.
92. McRee, D. E., Tainer, J. A., Meyer, T. E., van Beeumen, J., Cusanovich, M. A. & Getzoff, E. D. (1989). Proc. Natl Acad. Sci. USA, 86, 6533-6537.
93. Maiorov, V. & Abagyan, R. (1998). Fold. Des. 3, 259-269.
94. Marsh, R. E. (1995). Acta Cryst. B51, 897-907.
95. Marsh, R. E. (1997). Acta Cryst B53, 317-322.
96. Melo, F. & Feytmans, E. (1998). J. Mol. Biol. 277, 1141-1152.
97. Merritt, E. A. (1999). Acta Cryst. D55, 1109-1117.
98. Merritt, E. A., Kuhn, P., Sarfaty, S., Erbe, J. L., Holmes, R. K. & Hol, W. G. J. (1998). J. Mol. Biol. 282, 1043-1059.
99. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Proteins Struct. Funct. Genet. 12, 345-364.
100. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
101. Nayal, M. & Di Cera, E. (1996). J. Mol. Biol. 256, 228-234.
102. Noble, M. E. M., Zeelen, J. P., Wierenga, R. K., Mainfroid, V., Goraj, K., Gohimont, A. C. & Martial, J. A. (1993). Acta Cryst. D49, 403-417.
103. Nunn, R. S., Artymiuk, P. J., Baker, P. J. Rice, D. W. & Hunter, C. N. (1995). J. Mol. Biol. 252, 153-153.
104. Oldfield, T. J. & Hubbard, R. E. (1994). Proteins Struct. Funct. Genet. 18, 324-337.
105. Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J. (1998). Acta Cryst. D54, 1285-1294.
106. Pannu, N. S. & Read, R. J. (1996). Acta Cryst. A52, 659-668.
107. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). Acta Cryst. D52, 57-64.
108. Ponder, J. W. & Richards, F. M. (1987). J. Mol. Biol. 193, 775-791.
109. Pontius, J., Richelle, J. & Wodak, S. J. (1996). J. Mol. Biol. 264, 121-136.
110. Priestle, J. P. (1994). Structure, 2, 911-913.
111. Ramachandran, G. N. & Mitra, A. K. (1976). J. Mol. Biol. 107, 85-92.
112. Ramachandran, G. N. & Srinivasan, R. (1961). Nature (London), 190, 159-161.
113. Ramakrishnan, C. & Ramachandran, G. N. (1965). Biophys. J. 5, 909-933.
114. Read, R. J. (1986). Acta Cryst. A42, 140-149.
115. Read, R. J. (1990). Acta Cryst. A46, 900-912.
116. Read, R. J. (1994). Proceedings of the CCP4 Study Weekend. From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. A. Waller, pp. 31-40. Warrington: Daresbury Laboratory.
117. Read, R. J. (1997). Methods Enzymol. 277, 110-128.
118. Schomaker, V. & Trueblood, K. N. (1968). Acta Cryst. B24, 63-76.
119. Schultze, P. & Feigon, R. (1997). Nature (London), 387, 668-668.
120. Sevcik, J., Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1996). Acta Cryst. D52, 327-344.
121. Sheldrick, G. M. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 47-58. Warrington: Daresbury Laboratory.
122. Sinning, I., Kleywegt, G. J., Cowan, S. W., Reinemer, P., Dirr, H. W., Huber, R., Gilliland, G. L., Armstrong, R. N., Ji, X., Board, P. G., Olin, B., Mannervik, B. & Jones, T. A. (1993). J. Mol. Biol. 232, 192-212.
123. Sippl, M. J. (1993). Proteins Struct. Funct. Genet. 17, 355-362.
124. Stewart, D. E., Sarkar, A. & Wampler, J. E. (1990). J. Mol. Biol. 214, 253-260.
125. Stoddard, B. L., Howell, P. L., Ringe, D. & Petsko, G. A. (1990). Biochemistry, 29, 8885-8893.
126. Swindells, M. B., MacArthur, M. W. & Thornton, J. M. (1995). Nature Struct. Biol. 2, 596-603.
127. Taylor, R. & Kennard, O. (1986). Acta Cryst. B42, 112-120.
128. Ten Eyck, L. F. (1996). Proceedings of the CCP4 Study Wekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 37-45. Warrington: Daresbury Laboratory.
129. Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557.
130. Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). Acta Cryst. D55, 191-205.
131. Vellieux, F. M. D. A. P., Hunt, J. F., Roy, S. & Read, R. J. (1995). J. Appl. Cryst. 28, 347-351.
132. Vriend, G. (1990). J. Mol. Graph. 8, 52-56.
133. Vriend, G. & Sander, C. (1993). J. Appl. Cryst. 26, 47-60.
134. Walther, D. & Cohen, F. E. (1999). Acta Cryst. D55, 506-517.
135. Watkin, D. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 171-184. Warrington: Daresbury Laboratory.
136. Weaver, L. H., Tronrud, D. E., Nicholson, H. & Matthews, B. W. (1990). Curr. Sci. 59, 833-837.
137. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205.
138. Wilson, A. J. C. (1949). Acta Cryst. 2, 318-321.
139. Zou, J. Y. & Mowbray, S. L. (1994). Acta Cryst. D50, 237-249.