Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography

Journal of Synchrotron Radiation

Volumn 19, Issue 1, 2012, Pages 19-29

  Doutch, James ^a,b   Hough, Michael A ^a,c   Hasnain, S Samar ^a   Strange, Richard W ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b AUSTRALIAN NUCLEAR SCIENCE AND TECHNOLOGY ORGANISATION   (Australia)

^c UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

automated S SAD; Cu SAD; data redundancy; phasing; radiation damage; single wavelength anomalous diffraction

Indexed keywords

AUTOMATED S-SAD; CU-SAD; DATA REDUNDANCY; PHASING; SINGLE WAVELENGTH;

AMINO ACIDS; ATOMS; AUTOMATION; EXPERIMENTS; MINERALOGY; MODEL STRUCTURES; PROTEINS; RADIATION DAMAGE; SULFUR; SULFUR DETERMINATION; X RAY CRYSTALLOGRAPHY;

CRYSTAL ATOMIC STRUCTURE;

COPPER; NITRITE REDUCTASE; SULFUR;

ARTICLE; BETAPROTEOBACTERIA; CHEMISTRY; COMPUTER PROGRAM; CRYSTALLIZATION; ENZYMOLOGY; MACROMOLECULE; METHODOLOGY; SYNCHROTRON; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

BETAPROTEOBACTERIA; COPPER; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; MACROMOLECULAR SUBSTANCES; NITRITE REDUCTASES; SOFTWARE; SULFUR; SYNCHROTRONS; X-RAY DIFFRACTION;

EID: 84255167058     PISSN: 09090495     EISSN: 16005775     Source Type: Journal    
DOI: 10.1107/S0909049511049004     Document Type: Article

References (71)

1. Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse- Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C.,. Zwart, P. H. (2010). Acta Cryst. D66, 213-221.
2. 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.
3. Alkire, R.W., Duke, N. E. C., Rotella, F. J. (2008). J. Appl. Cryst. 41, 1122-1133.
4. Antonyuk, S. V., Hough, M. A. (2011). Biochim. Biophys. Acta, 1814, 778-784.
5. Antonyuk, S. V., Strange, R. W., Sawers, G., Eady, R. R., Hasnain, S. S. (2005). Proc. Natl Acad. Sci. 102, 12041-12046.
6. Behrens, W., Otto, H., Stuhrmann, H.B., Heyn, M. P. (1998). Biophys. J. 75, 255-263.
7. Boesecke, P., Bois, J. M., Crépin, T., Hunte, C., Kahn, R., Kao, W.-C., Nauton, L., Winther, A.-M. L., Moller, J., Nissen, P., Nury, H., Olesen, C., Pebay-Peyroula, E., Vicat, J., Stuhrmann, H. (2009). J. Synchrotron Rad. 16, 658-665.
8. Brockhauser, S., Di Michiel, M., McGeehan, J. E., McCarthy, A.A., Ravelli, R. B. G. (2008). J. Appl. Cryst. 41, 1057-1066.
9. Carpentier, P., Boesecke, P., Bois, J.-M., Chesne, M.-L., Fanchon, E., Kahn, R., Stuhrmann, H., Vicat, J. (2002). Acta Phys. Pol. 101, 603-612.
10. Cianci, M., Helliwell, J. R., Suzuki, A. (2008). Acta Cryst. D64, 1196-1209.
11. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
12. Cowtan, K. (1994). Jnt CCP4/ESF-EAMCB Newsl. Protein Crystallogr. 31, 34-38.
13. Dauter, Z. (2006). Acta Cryst. D62, 867-876.
14. Dauter, Z., Adamiak, D. A. (2001). Acta Cryst. D57, 990-995.
15. Dauter, Z., Dauter, M., de La Fortelle, E., Bricogne, G., Sheldrick, G. M. (1999). J. Mol. Biol. 289, 83-92.
16. Debreczeni, J.É., Bunkóczi, G., Ma, Q., Blaser, H., Sheldrick, G. M. (2003). Acta Cryst. D59, 688-696.
17. De la Mora, E., Carmichael, I., Garman, E. F. (2011). J. Synchrotron Rad. 18, 346-357.
18. Diederichs, K. (2010). Acta Cryst. D66, 733-740.
19. DjinovićCarugo, K., Helliwell, J. R., Stuhrmann, H., Weiss, M. S. (2005). J. Synchrotron Rad. 12, 410-419.
20. Ellis, M. J., Buffey, S. G., Hough, M.A., Hasnain, S. S. (2008). J. Synchrotron Rad. 15, 433-439.
21. Emsley, P., Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
22. Evans, P. (2006). Acta Cryst. D62, 72-82.
23. González, A., von Delft, F., Liddington, R. C., Bakolitsa, C. (2005). J. Synchrotron Rad. 12, 285-291.
24. Grosse-Kunstleve, R. W., Adams, P. D. (2003). Acta Cryst. D59, 1966-1973.
25. Heinrich, B., Bergamaschi, A., Broennimann, C., Dinapoli, R., Eikenberry, E. F., Johnson, I., Kobas, M., Kraft, P., Mozzanica, A., Schmitt, B. (2009). Nucl. Instrum. Methods Phys. Res. A, 607, 247-249.
26. Helliwell, J. R. (1992). Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press.
27. Hendrickson, W.A., Teeter, M. M. (1981). Nature (London), 290, 107-113.
28. Hough, M. A., Antonyuk, S. V., Strange, R. W., Eady, R. R., Hasnain, S. S. (2008). J. Mol. Biol. 378, 353-361.
29. Hülsen, G., Broennimann, C., Eikenberry, E. F., Wagner, A. (2006). J. Appl. Cryst. 39, 550-557.
30. Kabsch, W. (2010). Acta Cryst. D66, 125-132.
31. Kim, C. U., Hao, Q., Gruner, S. M. (2007). Acta Cryst. D63, 653-659.
32. Kitago, Y., Watanabe, N., Tanaka, I. (2005). Acta Cryst. D61, 1013-1021.
33. Kitago, Y., Watanabe, N., Tanaka, I. (2010). J. Appl. Cryst. 43, 341-346.
34. Langer, G., Cohen, S. X., Lamzin, V.S., Perrakis, A. (2008). Nat. Protoc. 3, 1171-1179.
35. Lemke, C. T., Smith, G.D., Howell, P. L. (2002). Acta Cryst. D58, 2096-2101.
36. Leslie, A. G. W. (1992). Jnt CCP4/ESF-EAMCB Newsl. Protein Crystallogr. 26, 27-33.
37. Liu, Q., Zhang, Z., Hendrickson, W. A. (2011). Acta Cryst. D67, 45-59.
38. Liu, Z. J., Vysotski, E. S., Chen, C. J., Rose, J. P., Lee, J. &Wang, B. C. (2000). Protein Sci. 9, 2085-2093.
39. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
40. Mooij, W. T., Cohen, S. X., Joosten, K., Murshudov, G. N., Perrakis, A. (2009). Structure, 17, 183-189.
41. Morris, R. J., Perrakis, A., Lamzin, V. S. (2003). Methods Enzymol. 374, 229-244.
42. Mueller-Dieckmann, C., Panjikar, S., Schmidt, A., Mueller, S., Kuper, J., Geerlof, A., Wilmanns, M., Singh, R. K., Tucker, P.A., Weiss,M. S. (2007). Acta Cryst. D63, 366-380.
43. Mueller-Dieckmann, C., Panjikar, S., Tucker, P.A., Weiss, M. S. (2005). Acta Cryst. D61, 1263-1272.
44. Murshudov, G. N., Vagin, A.A., Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
45. Nan, J., Zhou, Y., Yang, C., Brostromer, E., Kristensen, O., Su, X.-D. (2009). Acta Cryst. D65, 440-448.
46. Orville, A. M., Buono, R., Cowan, M., Héroux, A., Shea-McCarthy, G., Schneider, D. K., Skinner, J. M., Skinner, M. J., Stoner-Ma, D., Sweet, R. M. (2011). J. Synchrotron Rad. 18, 358-366.
47. Otwinowski, Z., Minor, W. (1997). Macromolecular Crystallography, Part A, edited by C. W. Carter and R. M. Sweet, pp. 307-326. New York: Academic Press.
48. Owen, R. L., Pearson, A. R., Meents, A., Boehler, P., Thominet, V., Schulze-Briese, C. (2009). J. Synchrotron Rad. 16, 173-182.
49. Paithankar, K. S., Owen, R.L., Garman, E. F. (2009). J. Synchrotron Rad. 16, 152-162.
50. Perrakis, A., Morris, R., Lamzin, V. S. (1999). Nat. Struct. Biol. 6, 458-463.
51. Polentarutti, M., Glazer, R., DjinovićCarugo, K. (2004). J. Appl. Cryst. 37, 319-324.
52. Ramagopal, U. A., Dauter, M., Dauter, Z. (2003). Acta Cryst. D59, 1020-1027.
53. Ravelli, R.B., Garman, E. F. (2006). Curr. Opin. Struct. Biol. 16, 624-629.
54. Ravelli, R. B. G., Nanao, M. H., Lovering, A., White, S., McSweeney, S. (2005). J. Synchrotron Rad. 12, 276-284.
55. Sarma, G. N., Karplus, P. A. (2006). Acta Cryst. D62, 707-716.
56. Schneider, T. R., Sheldrick, G. M. (2002). Acta Cryst. D58, 1772-1779.
57. Sheldrick, G. M. (2002). Z. Kristallogr. 217, 644-650.
58. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
59. Stoner-Ma, D., Skinner, J. M., Schneider, D. K., Cowan, M., Sweet, R.M., Orville, A. M. (2011). J. Synchrotron Rad. 18, 37-40.
60. Strange, R.W., Ellis, M.J., Hasnain, S. S. (2005). Coord. Chem. Rev. 249, 197-208.
61. Stuhrmann, S., Bartels, K. S., Braunwarth, W., Doose, R., Dauvergne, F., Gabriel, A., Knöchel, A., Marmotti, M., Stuhrmann, H. B., Trame, C., Lehmann, M. S. (1997). J. Synchrotron Rad. 4, 298-310.
62. Terwilliger, T. (2004). J. Synchrotron Rad. 11, 49-52.
63. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N.W., Zwart, P. H., Hung, L.-W., Read, R.J., Adams, P. D. (2008). Acta Cryst. D64, 61-69.
64. Usón, I., Stevenson, C. E. M., Lawson, D.M., Sheldrick, G. M. (2007). Acta Cryst. D63, 1069-1074.
65. Wang, B. C. (1985). Diffraction Methods for Biological Macromolecules, pp. 90-112. New York: Academic Press.
66. Wang, J., Dauter, M., Dauter, Z. (2006). Acta Cryst. D62, 1475-1483.
67. Watanabe, N., Kitago, Y., Tanaka, I., Wang, J., Gu, Y., Zheng, C., Fan, H. (2005). Acta Cryst. D61, 1533-1540.
68. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
69. Weiss, M. S., Sicker, T., Djinovic-Carugo, K., Hilgenfeld, R. (2001). Acta Cryst. D57, 689-695.
70. Weiss, M. S., Sicker, T., Hilgenfeld, R. (2001). Structure, 9, 771-777.
71. Yang, C., Pflugrath, J. W., Courville, D. A., Stence, C. N., Ferrara, J. D. (2003). Acta Cryst. D59, 1943-1957.