Development of instrumentation and methods for MAD and structural genomics at the SRS, ESRF, CHESS and Elettra facilities

Journal of Synchrotron Radiation

Volumn 6, Issue 4, 1999, Pages 822-833

  Cassetta, Alberto ^a   Deacon, Ashley M ^d   Ealick, Steve E ^d   Helliwell, John R ^b   Thompson, Andrew W ^c  

^a CNR   (Italy)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (France)

^d NONE

Author keywords

Genomics; Multiwavelength anomalous dispersion (MAD); Protein crystallography; Proteomics

Indexed keywords

EID: 0033462391     PISSN: 09090495     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0909049599006172     Document Type: Article

References (110)

1. Abrahams, J. P., Leslie. A. G. W., Lutter, R. & Walker, J. E. (1994). Nature (London), 370, 621-628.
2. Acharya, R., Fry, E., Stuart, D., Fox, G., Rowlands, D. & Brown, F. (1989). Nature (London), 337, 709-716.
3. Adams, M. J., Helliwell, J. R. & Bugg, C. E. (1977). J. Mol. Biol. 112, 183-197.
4. Ævarsson, A., Seger, K., Turley, S., Sokatch, J. R. & Hol, W. G. J. (1999). Nat. Struct. Biol. In the press.
5. Arndt, U. W., Greenhough. T. J., Helliwell, J. R., Howard, J. A. K., Rule, S. A. & Thompson, A. W. (1982). Nature (London), 298, 835-838.
6. Arndt, U. W. & Wonacott, A. J. (1977). The Rotation Method in Crystallography. Amsterdam: North Holland.
7. Bailey, S., Smith, K., Fairlamb, A. H. & Hunter, W. N. (1993). Eur. J. Biochem. 213, 67-75.
8. Baker, P. J., Farrants, G. W., Stillman, T. J., Britton, K. L., Helliwell, J. R. & Rice, D. W. (1990). Acta Cryst. A46, 721-725.
9. Bernstorff, S., Busetto, E., Gramaccioni, C., Lausi, A., Olivi, L., Zanini, F., Savoia, A., Colapietro, M., Portalone, G., Camalli, M., Pifferi, A., Spagna, R., Barba, L. & Cassetta, A. (1995). Rev. Sci. Instrum. 66(2), 1661-1664.
10. Bernstorff, S., Busetto, E., Savoia, A. & Colapietro, M. (1995). Rev. Sci. Instrum. 66(2), 2065-2068.
11. Blessing, R. H. & Smith, G. D. (1999). J. Appl. Cryst. In the press.
12. Bourgeois, D., Ursby, T., Wulff, M., Pradervand, C., Legrand, A., Schildkamp, W., Laboure, S., Srajer, V., Teng, T. Y., Roth, M. & Moffat, K. (1996). J. Synchrotron Rad. 3, 65-74.
13. Brammer, R. C., Helliwell, J. R., Lamb, W., Liljas, A., Moore, P. R., Thompson, A. W. & Rathbone, K. (1988). Nucl. Instrum. Methods, A271, 678-687.
14. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
15. Bugg, C. E., Carson. W. M. & Montgomery, J. A. (1993). Sci. Am. 12, 60-66.
16. Bujacz, G., Jaskoski, M., Alexandratos, J., Wlodawer, A., Merkel, G., Katz, R. A. & Skalka, A. M. (1995). J. Mol. Biol. 253, 333-346.
17. Chayen, N. & Helliwell, J. R. (1998). Phys. World, 5, 43-48.
18. Chayen, N. E., Boggon, T. J., Cassetta, A., Deacon, A., Gleichmann, T., Habash, J., Harrop, S. J., Helliwell, J. R., Nieh, Y. P., Peterson, M. R., Raftery, J., Snell, E. H., Hädener, A., Niemann, A. C., Siddons, D. P., Stojanoff, V., Thompson, A. W., Ursby, T. & Wulff, M. (1996). Q. Rev. Biophys. 29(3), 227-278.
19. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
20. Das, S., Yu, L. H., Gaitatzes, C., Rogers, R., Freeman, J., Bienkowska, J., Adams, R. M., Smith, T. F. & Lindellen, J. (1997). Nature (London), 385, 29-30.
21. Deacon, A., Gleichmann, T., Kalb, A. J., Price, H., Raftery, J., Bradbrook, G., Yariv, J. & Helliwell, J. R. (1997). J. Chem. Soc. Faraday Trans. 93(24), 4305-4312.
22. Deacon, A., Habash, J., Harrop, S. J., Helliwell, J. R., Hunter, W. N., Leonard, G. A., Peterson, M., Hädener, A., Kalb, A. J., Allinson, N. M., Castelli, C., Moon, K., McSweeney, S., Gonzalez, A., Thompson, A. W., Ealick, S., Szebenyi, D. M. & Walter, R. (1995). Rev. Sci. Instrum. 66(2), 1287-1292.
23. Deacon, A. M., Ni, Y., Coleman, W. G. Jr & Ealick, S. E. (1999). Private communication.
24. Deacon, A. M., Weeks, C. M., Miller, R. & Ealick, S. E. (1998). Proc. Natl Acad. Sci. USA, 95, 9284-9289.
25. Doublié, S. (1997). Methods Enzymol. 276, 523-530.
26. Duke, E. M. H., Kehoe, R. C., Rizkallah, P. J., Clarke, J. A. & Nave, C. (1998). J. Synchrotron Rad. 5, 497-499.
27. Ealick, S. E., Rule, S. A., Carter, D. C., Greenhough, T. J., Babu, Y. S., Cook, W. J., Habash, J., Helliwell, J. R., Stoeckler, J. D., Parks, R. E. Jr, Chen, S. & Bugg, C. E. (1990). J. Biol. Chem. 265, 1812-1820.
28. Einspahr, H., Suguna, K., Suddath, F. L., Ellis, G., Helliwell, J. R. & Papiz, M. Z. (1985). Acta Cryst. B41, 336-341.
29. Ekstrom, J. L., Mathews, I. I., Stanley, B. A., Pegg, A. E. & Ealick, S. E. (1999). Structure, 7, 583-595.
30. Evans, G. & Wilson, K. S. (1999). Acta Cryst. D55, 67-76.
31. Fourme, R., Shepard, W., Schiltz, M., Prangé, T., Ramin, M., Kahn, R., de la Fortelle, E. & Bricogne, G. (1999). J. Synchrotron Rad. 6, 834-844.
32. Frazão, C., Sieker, L., Sheldrick, G. M., Lamzin, V., LeGall, J. & Corrondo, M. A. (1999). J. Bioinorg. Chem. In the press.
33. Friedman, A. M., Fischmann, T. O. & Steitz, T. A. (1995). Science, 268, 1721-1727.
34. Glover, I. D., Denny, R. C., Nguti, N. D., McSweeney, S. M., Kinder, S. H., Thompson, A. W., Dodson, E. J., Wilkinson, A. J. & Tame, J. R. H. (1995). Acta Cryst. D51, 39-47.
35. Greenhough, T. J. & Helliwell, J. R. (1982). J. Appl. Cryst. 15, 493-508.
36. Grimes, J. M., Jakana, J., Ghosh, M., Basak, A. K., Roy, P., Chiu, W., Stuart, D. I. & Prasad, B. V. V. (1997). Structure, 5, 885-893.
37. Guss, J. M., Merrit, E. A., Phizackerley, R. P., Hedman, B., Murata, M., Hodgson, K. O. & Freeman, H. C. (1988). Science, 241, 806-811.
38. Hädener, A., Matzinger, P. K., Battersby, A. R., McSweeney, S., Thompson, A. W., Hammersley, A. P., Harrop, S. J., Cassetta, A., Deacon, A., Hunter, W. N., Nieh, Y. P., Raftery, J., Hunter, N. & Helliwell, J. R. (1999). Acta Cryst. D55, 631-643.
39. Haslegrove, J. C., Faruqi, A. R., Huxley, H. E. & Arndt, U. W. (1977). J. Phys. E, 10, 1035-1044.
40. Hasnain, S. S. & Hodgson, K. O. (1999). J. Synchrotron Rad. 6, 852-864.
41. Hauptman, H. A. (1995). Crystallographic Computing 5: From Chemistry to Biology, edited by D. Moras, A. D. Podjarny & J. C. Thierry, pp. 324-332. IUCr/Oxford University Press.
42. Hedman, B., Hodgson, K. O., Helliwell, J. R., Liddington, R. & Papiz, M. Z. (1985). Proc. Natl Acad. Sci. USA, 82, 7604-7607.
43. Helliwell, J. R. (1977a). New Sci. 76, 646-648.
44. Helliwell, J. R. (1977b). DPhil thesis, Oxford University, UK.
45. Helliwell, J. R. (1979). Proceedings of Daresbury Study Weekend, DL/Sci/R13, pp. 1-6, 26-28 January 1979. Warrington: Daresbury Laboratory.
46. Helliwell, J. R. (1984). Rep. Prog. Phys. 47, 1403-1497.
47. Helliwell, J. R. (1985). J. Mol. Struct. 130, 63-91.
48. Helliwell, J. R. (1987). ESRF Foundation Phase Report. ESRF, Grenoble, France.
49. Helliwell, J. R. (1992). Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press.
50. Helliwell, J. R. (1998). Nat. Struct. Biol. (Synchrotron Suppl.), pp. 614-617.
51. Helliwell, J. R., Cruickshank, D. W. J., Ellis, G., Habash, J., Papiz, M. Z. & Rule, S. A. (1984). Proceedings of Daresbury Study Weekend, DL/Sci/R22, pp. 41-59. Warrington: Daresbury Laboratory.
52. Helliwell, J. R. & Fourme, R. (1983). Report to ESRP, Geneva.
53. Helliwell, J. R., Greenhough, T. J., Carr, P., Rule, S. A., Moore, P. R., Thompson, A. W. & Worgan, J. S. (1982). J. Phys. E, 15, 1363-1372.
54. Helliwell, J. R., Papiz, M. Z., Glover, I. D., Habash, J., Thompson, A. W., Moore, P. R., Harris, N., Croft, D. & Pantos, E. (1986). Nucl. Instrum. Methods, A246, 617-623.
55. Helliwell, J. R. & Rentzepis, P. M. (1997). Editors. Time-Resolved Diffraction. Oxford University Press.
56. Helliwell, M., Helliwell, J. R., Kaucic, V., Zabukovec Logar, N., Barba, L., Busetto, E. & Lausi, A. (1999). Acta Cryst. B55, 327-332.
57. Hendrickson, W. A. (1985). Trans. Am. Cryst. Assoc. 21, 11-21.
58. Hendrickson, W. A. (1991). Science, 254, 51-58.
59. Hendrickson, W. A. (1999). J. Synchrotron Rad. 6, 845-851.
60. Hendrickson, W. A., Horton, J. R. & Lemaster, D. M. (1990). EMBO J. 9(5), 1665-1672.
61. Herzenberg, A. & Lau, H. S. M. (1967). Acta Cryst. 22, 24-28.
62. Hope, H. (1988). Acta Cryst. B44, 22-26.
63. Hoppe, W. & Jakubowski, U. (1975). Anomalous Scattering, edited by S. Ramaseshan & S. C. Abrahams, pp. 437-461. Copenhagen: Munksgaard.
64. Hunter, N. S., Gleichmann, T. J., Helliwell, M., Barba, L., Busetto, E., Lausi, A., Price, H. J. & Helliwell, J. R. (1999). Croat. Chem. Acta. In the press.
65. Kahn, J. M. & Smith, J. L. (1999). Private communication.
66. Kahn, R., Fourme, R., Bosshard, R., Chiadmi, M., Risler, J. L., Dideberg, O. & Wery, J. P. (1985). FEBS Lett. 179(1), 133-137.
67. Kalb, A. J., Habash, J., Hunter, N. S., Price, H. J., Raftery, J. & Helliwell, J. R. (1999). Metals Biol. 37. In the press.
68. Kauppi, B., Lee, K., Carredano, E., Parales, R. E., Gibson, D. T., Eklund, H. & Ramaswamy, S. (1998). Structure, 6, 571-586.
69. Laboure, S., Leonard, G., Stojanoff, V., Svensson, O. & Thompson, A. W. (1999). ESRF Annual Reports and Highlights. ESRF, Grenoble, France.
70. Leahy, D. J., Hendrickson, W. A., Aukhil, I. & Erickson, H. P. (1992). Science, 258, 987-991.
71. Lebioda, L., Radfar, R., Shin, R., Sheldrick, G. M., Odom, J. D. & Dunlap, R. B. (1999). Personal communication.
72. Lemonnier, M., Fourme, R., Rousseaux, F. & Kahn, R. (1978). Nucl. Instrum. Methods, 152, 173-177.
73. Li, C., Kappock, T. J., Stubbe, J. & Ealick, S. E. (1999). Structure. In the press.
74. Liddington, R. C., Yan, Y., Moulai, J., Sahli, R., Benjamin, T. L. & Harrison, S. C. (1991). Nature (London), 354, 278-284.
75. Mukherjee, A., Helliwell, J. R. & Main, P. (1989). Acta Cryst. A45, 715-718.
76. Newman, M., Strzelecka, T., Domer, L. F., Schildkraut, I. & Aggarwal, A. K. (1994). Nature (London), 368, 660-664.
77. Nieh, Y. P. & Helliwell, J. R. (1995). J. Synchrotron Rad. 2, 79-82.
78. Ogata, C. M. (1998). Nat. Struct. Biol. (Synchrotron Suppl.), 5, 638-640.
79. Okaya, Y. & Pepinsky, R. (1956). Phys. Rev. 103, 1645.
80. Peterson, M. R., Harrop, S. J., McSweeney, S. M., Leonard, G. A., Thompson, A. W., Hunter, W. N. & Helliwell, J. R. (1996). J. Synchrotron Rad. 3, 24-34.
81. Ren, Z., Bourgeois, D., Helliwell, J. R., Srajer, V., Stoddard, B. L. & Moffat, K. (1999). J. Synchrotron Rad. 6, 891-917.
82. Rizkallah, P. J. (1999). Protein Crystallography Publications, http:// www.dl.ac.uk/SRS/PX/publications.html.
83. Rodgers, D. W. (1994). Structure, 2, 1135-1140.
84. Rossmann, M. G. (1999). J. Synchrotron Rad. 6, 816-821.
85. Shamoo, Y., Friedman, A. M., Parsons, M. R., Konigsberg, W. H. & Steitz, T. A. (1995). Nature (London), 376, 362-366.
86. Sheldrick, G. M. (1998). Direct Methods for Solving Structures, edited by S. Fortier, pp. 401-411. Dordecht: Kluwer.
87. Sinha, S., Krahn, J. M., Shin, B. S., Tomchick, D. R., Zalkin, H. & Smith, J. L. (1998). ACA Meeting, Arlington, 18-23 July 1998. W0012.
88. Smith, G. D., Nagar, B., Rini, J. M., Hauptman, H. A. & Blessing, R. H. (1998). Acta Cryst. D54, 799-804.
89. Smith, J. L. & Thompson, A. W. (1998). Structure, 6(7), 815-819.
90. Smolenski, K. W., Shen, Q. & Doing, P. (1997). Proc. SPIE, 3151, 181-187.
91. Szebenyi, D. M. E., Arvai, A., Ealick, S., LaIuppa, J. M. & Nielsen, C. (1997). J. Synchrotron Rad. 4, 128-135.
92. Tate, M. R., Eikenberry, E. F., Barna, S. L., Wall, M. E., Lawrence, J. L. & Gruner, S. M. (1995). J. Appl. Cryst. 28, 196-205.
93. Teng, T. Y. (1990). J. Appl. Cryst. 23, 387-391.
94. Terwilliger, T. C. & Berendzen, J. (1999). Acta Cryst. In the press.
95. Terwilliger, T. C., Kim, S.-H. & Eisenberg, D. (1987). Acta Cryst. A43, 1-5.
96. Thanos, C. D., Goodwill, K. E. & Bowie, J. U. (1999). Science, 282, 833-836.
97. Thiel, D. J., Blank, B. & LaIuppa, J. (1998). J. Synchrotron Rad. 5, 914-916.
98. Thiel, D. J., Ealick, S. E., Tate, M. W., Gruner, S. M. & Eikenberry, E. F. (1996). Rev. Sci. Instrum. 67, 1.
99. Thiel, D. J., le Du, M., Walter, R. L., D'Arcy, A., Chene, C., Fontoulakis, M., Garotta, G., Winkler, F. & Ealick, S. E. (1995). 5th International Conference on Biophysics and Synchrotron Radiation, Grenoble, France. Abstract 01/38.
100. Thompson, A. W., Habash, J., Harrop, S., Helliwell, J. R., Nave, C., Atkinson, P., Hasnain, S. S., Glover, I. D., Moore, P. R., Harris, N., Kinder, S. & Buffey, S. (1992). Rev. Sci. Instrum. 63(1), 1062-1064.
101. Timm, D. E. (1999). Private communication.
102. Todd, A. K., Adams, A., Powell, H. R., Wilcock, D. J., Thorpe, J. H., Lausi, A., Zanini, F., Wakelin, L. P. G. & Cardin, C. J. (1999). Acta Cryst. D55. 729-735.
103. Turner, M. A., Yuan, C.-S., Borchardt, R. T., Hershfield, M. S., Smith, G. D. & Howell, P. L. (1998). Nat. Struct. Biol. 5, 369-376.
104. Wakatsuki, S., Belrhali, H., Mitchell, E. P., Burmeister, W. P., McSweeney, S. M., Kahn, R., Bourgeois, D., Yao, M., Tomizaki, T. & Theveneau, P. (1998). J. Synchrotron Rad. 5, 215-221.
105. Walsh, M. A., Otwinowski, Z., Perrakis, A., Anderson, P. M. & Joachimiak, A. (1999). Private communication.
106. Walter, R. L., Ealick, S. E., Friedman, A. M., Blake, R. C., Proctor, P. & Shoham, M. (1996). J. Mol. Biol. 263, 730-751.
107. Walter, R. L., Thiel, D. J., Barna, S. L., Tate, M. W., Eikenberry, E. F., Gruner, S. M. & Ealick, S. E. (1995). Structure, 3, 835-844.
108. Weeks, C. M. & Miller, R. (1999). J. Appl. Cryst. 32, 120-124.
109. Weeks, C. M., Sheldrick, G. M., Miller, R., Uson, I. & Hauptman, H. A. (1999). Bull. Czech Slovak Crystallogr. Assoc. In the press.
110. Wilson, K. S. (1978). Acta Cryst. A45, 718-726.