Gyre and gimble: A maximum-likelihood replacement for patterson correlation refinement

Acta Crystallographica Section D: Structural Biology

Volumn 74, Issue 4, 2018, Pages 279-289

  McCoy, Airlie J ^a   Oeffner, Robert D ^a   Millán, Claudia ^b   Sammito, Massimo ^b   Usón, Isabel ^b,c   Read, Randy J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

Antibodies; Crystallographic phasing; Fragment based molecular replacement; Maximum likelihood; Patterson correlation refinement

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT;

CHEMISTRY; HUMAN; MOLECULAR MODEL; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; ROTATION; SOFTWARE; STATISTICAL MODEL; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; LIKELIHOOD FUNCTIONS; MODELS, MOLECULAR; PROTEIN CONFORMATION; ROTATION; SOFTWARE;

EID: 85045402056     PISSN: None     EISSN: 20597983     Source Type: Journal    
DOI: 10.1107/S2059798318001353     Document Type: Article

References (37)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213–221.
2. Adams, P. D. et al. (2011). Methods, 55, 94–106.
3. 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.
4. Brünger, A. T. (1990). Acta Cryst. A46, 46–57.
5. Brünger, A. T. (1991). Acta Cryst. A47, 195–204.
6. Brünger, A. T. (1992). X-PLOR v.3.1. A System For X-ray Crystallography and NMR. New Haven: Yale University Press.
7. Brünger, A. T. (1993). ImmunoMethods, 3, 180–190.
8. Brünger, 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.
9. Bunkóczi, G. & Read, R. J. (2011). Acta Cryst. D67, 303–312.
10. Carroll, L. (1871). Through the Looking-Glass, and What Alice Found There. London: Macmillan.
11. Cohen, G. H., Sheriff, S. & Davies, D. R. (1996). Acta Cryst. D52, 315–326.
12. Cohen, G. H., Silverton, E. W., Padlan, E. A., Dyda, F., Wibbenmeyer, J. A., Willson, R. C. & Davies, D. R. (2005). Acta Cryst. D61, 628–633.
13. DeLano, W. L. (2002). PyMOL. http://www.pymol.org.
14. Echols, N., Grosse-Kunstleve, R. W., Afonine, P. V., Bunkóczi, G., Chen, V. B., Headd, J. J., McCoy, A. J., Moriarty, N. W., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. & Adams, P. D. (2012). J. Appl. Cryst. 45, 581–586.
15. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501.
16. Fujinaga, M. & Read, R. J. (1987). J. Appl. Cryst. 20, 517–521.
17. Harzing, A.-W. K. & van der Wal, R. (2008). Ethics Sci. Environ. Polit. 8, 61–73.
18. Jeffrey, P. D., Strong, R. K., Sieker, L. C., Chang, C. Y., Campbell, R. L., Petsko, G. A., Haber, E., Margolies, M. N. & Sheriff, S. (1993). Proc. Natl Acad. Sci. USA, 90, 10310–10314.
19. Krissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256–2268.
20. McCoy, A. J. (2017). Methods Mol. Biol. 1607, 421–453.
21. 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.
22. McCoy, A. J., Nicholls, R. A. & Schneider, T. R. (2013). Acta Cryst. D69, 2216–2225.
23. McCoy, A. J., Read, R. J., Bunkóczi, G. & Oeffner, R. D. (2009). Phaserwiki. http://www.phaser.cimr.cam.ac.uk.
24. Millán, C., Sammito, M. D., McCoy, A. J., Ziem Nascimento, A. F., Petrillo, G., Oeffner, R. D., Domínguez-Gil, T., Hermoso, J. A., Read, R. J. & Usón, I. (2018). Acta Cryst. D74, 290–304.
25. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355–367.
26. Oeffner, R. D., Bunkóczi, G., McCoy, A. J. & Read, R. J. (2013). Acta Cryst. D69, 2209–2215.
27. Read, R. J. (1986). Acta Cryst. A42, 140–149.
28. Read, R. J. (2001). Acta Cryst. D57, 1373–1382.
29. Read, R. J. & McCoy, A. J. (2016). Acta Cryst. D72, 375–387.
30. Sammito, M., Meindl, K., de Ilarduya, I. M., Millán, C., Artola-Recolons, C., Hermoso, J. A. & Usón, I. (2014). FEBS J. 281, 4029–4045.
31. Sammito, M., Millán, C., Rodríguez, D. D., de Ilarduya, I. M., Meindl, K., De Marino, I., Petrillo, G., Buey, R. M., de Pereda, J. M., Zeth, K., Sheldrick, G. M. & Usón, I. (2013). Nature Methods, 10, 1099–1101.
32. Schwarzenbacher, R., Godzik, A., Grzechnik, S. K. & Jaroszewski, L. (2004). Acta Cryst. D60, 1229–1236.
33. Sheldrick, G. M. (2010). Acta Cryst. D66, 479–485.
34. Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smith-Gill, S. J., Finzel, B. C. & Davies, D. R. (1987). Proc. Natl Acad. Sci. USA, 84, 8075–8079.
35. Storoni, L. C., McCoy, A. J. & Read, R. J. (2004). Acta Cryst. D60, 432–438.
36. Terwilliger, T. C., Read, R. J., Adams, P. D., Brunger, A. T., Afonine, P. V. & Hung, L.-W. (2013). Acta Cryst. D69, 2244–2250.
37. Yeates, T. O. & Rini, J. M. (1990). Acta Cryst. A46, 352–359.