Do we see what we should see? Describing non-covalent interactions in protein structures including precision

IUCrJ

Volumn 1, Issue , 2014, Pages 74-81

  Gurusaran, Manickam ^a   Shankar, Mani ^a   Nagarajan, Raju ^a   Helliwell, John R ^b   Sekar, Kanagaraj ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

crystal structure analysis; diffraction component precision index; DPI; full matrix least squares method; measurement uncertainty; neutron diffraction; protein crystal structure precision; salt bridges

Indexed keywords

EID: 84926160533     PISSN: None     EISSN: 20522525     Source Type: Journal    
DOI: 10.1107/S2052252513031485     Document Type: Article

References (24)

1. Ahmed, H. U., Blakeley, M. P., Cianci, M., Cruickshank, D. W. J., Hubbard, J. A. & Helliwell, J. R. (2007). Acta Cryst. D63, 906-922.
2. Barlow, D. J. & Thornton, J. M. (1983). J. Mol. Biol. 168, 867-885.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.
4. Blow, D. M. (2002). Acta Cryst. D58, 792-797.
5. Burkhard, P., Kammerer, R. A., Steinmetz, M. O., Bourenkov, G. P. & Aebi, U. (2000). Structure, 8, 223-230.
6. Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
7. Deacon, A., Gleichmann, T., Kalb (Gilboa), A. J., Price, H., Raftery, J., Bradbrook, G., Yariv, J. & Helliwell, J. R. (1997). J. Chem. Soc. Faraday Trans. 93, 4305-4312.
8. Effler, J. C., Iglesias, P. A. & Robinson, D. N. (2006). Control of Uncertain Systems: Modelling, Approximation, and Design, edited by B. A. Francis, M. C. Smith & J. C. Willems, pp. 203-224. Berlin, Heidelberg: Springer-Verlag.
9. Fersht, A. R. (1972). J. Mol. Biol. 64, 497-509.
10. Fisher, S. J., Blakeley, M. P., Cianci, M., McSweeney, S. & Helliwell, J. R. (2012). Acta Cryst. D68, 800-809.
11. Fisher, S. J., Helliwell, J. R., Khurshid, S., Govada, L., Redwood, C., Squire, J. M. & Chayen, N. E. (2008). Acta Cryst. D64, 658-664.
12. Gowri Shankar, B. A., Sarani, R., Michael, D., Mridula, P., Ranjani, C. V., Sowmiya, G., Vasundhar, B., Sudha, P., Jeyakanthan, J., Velmurugan, D. & Sekar, K. (2007). J. Biosci. 32, 693-704.
13. Hsin, K., Sheng, Y., Harding, M. M., Taylor, P. & Walkinshaw, M. D. (2008). J. Appl. Cryst. 41, 963-968.
14. Kumar, S., Ma, B., Tsai, C.-J. & Nussinov, R. (2000). Proteins, 38, 368-383.
15. Kumar, S. & Nussinov, R. (2002). Biophys. J. 83, 1595-1612.
16. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
17. 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.
18. Musafia, B., Buchner, V. & Arad, D. (1995). J. Mol. Biol. 254, 761-770.
19. Perutz, M. F. (1970). Nature (London), 228, 726-739.
20. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
21. Tanley, S. W. M., Schreurs, A. M. M., Kroon-Batenburg, L. M. J., Meredith, J., Prendergast, R., Walsh, D., Bryant, P., Levy, C. & Helliwell, J. R. (2012). Acta Cryst. D68, 601-612.
22. Thoden, J. B., Marti-Arbona, R., Raushel, F. M. & Holden, H. M. (2003). Biochemistry, 42, 4874-4882.
23. Williams, R. S., Boeckeler, K., Gräf, R., Müller-Taubenberger, A., Li, Z., Isberg, R. R., Wessels, D., Soll, D. R., Alexander, H. & Alexander, S. (2006). Trends Mol. Med. 12, 415-424.
24. Xu, D., Tsai, C.-J. & Nussinov, R. (1997). Protein Eng. 10, 999-1012.