Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (original) (raw)

References

First citationAdams, P. D. et al. (2010). Acta Cryst. D66, 213–221. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationAfonine, P., Grosse-Kunstleve, R. & Adams, P. (2005). CCP4 Newsl. Protein Crystallogr. 42, contribution 8. Google Scholar
First citationBerman, H., Henrick, K. & Nakamura, H. (2003). Nature Struct. Biol. 10, 980. Web of Science CrossRef PubMed Google Scholar
First citationBradley, P., Misura, K. M. & Baker, D. (2005). Science, 309, 1868–1871. Web of Science CrossRef PubMed CAS Google Scholar
First citationBricogne, G., Blanc, E., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Roversi, P., Sharff, A., Smart, O. & Vonrhein, C. (2010). BUSTER. Cambridge: Global Phasing Ltd. Google Scholar
First citationBrünger, A. T. (1992_a_). X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. New Haven: Yale University Press. Google Scholar
First citationBrünger, A. T. (1992_b_). Nature (London), 355, 472–475. PubMed Web of Science Google Scholar
First citationBrunger, A. T. (2007). Nature Protoc. 2, 2728–2733. Web of Science CrossRef CAS Google Scholar
First citationBrünger, 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. Web of Science CrossRef IUCr Journals Google Scholar
First citationChen, V. B. (2010). PhD thesis, Duke University, USA. Google Scholar
First citationChen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12–21. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationChen, V. B., Davis, I. W. & Richardson, D. C. (2009). Protein Sci. 18, 2403–2409. Web of Science CrossRef PubMed CAS Google Scholar
First citationDennis, J. E. Jr & Welsch, R. E. (1978). Commun. Stat. Simul. Comput. 7, 345–359. CrossRef Google Scholar
First citationEmsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationEngh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392–400. CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationFabiola, F., Bertram, R., Korostelev, A. & Chapman, M. S. (2002). Protein Sci. 11, 1415–1423. Web of Science CrossRef PubMed CAS Google Scholar
First citationGeman, S. A. & McClure, D. E. (1987). Bull Int. Stat. Inst. 52, 5–21. Google Scholar
First citationHeadd, J. J. (2009). PhD thesis, Duke University, USA. Google Scholar
First citationHeadd, J. J., Immormino, R. M., Keedy, D. A., Emsley, P., Richardson, D. C. & Richardson, J. S. (2009). J. Struct. Funct. Genomics, 10, 83–93. CrossRef PubMed CAS Google Scholar
First citationHintze, B. J. & Johnson, S. J. (2010). J. Appl. Cryst. 43, 1540–1542. CrossRef CAS IUCr Journals Google Scholar
First citationKabsch, W. & Sander, C. (1983). Biopolymers, 22, 2577–2637. CrossRef CAS PubMed Web of Science Google Scholar
First citationKarmali, A. M., Blundell, T. L. & Furnham, N. (2009). Acta Cryst. D65, 121–127. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationKim, J. J., Casteel, D. E., Huang, G., Kwon, T. H., Ren, R. K., Zwart, P., Headd, J. J., Brown, N. G., Chow, D.-C., Palzkill, T. & Kim, C. (2011). PLoS One, 6, e18413. CrossRef PubMed Google Scholar
First citationKleywegt, G. J. & Brünger, A. T. (1996). Structure, 4, 897–904. CrossRef CAS PubMed Web of Science Google Scholar
First citationKleywegt, G. J. & Jones, T. A. (1996). Structure, 4, 1395–1400. CrossRef CAS PubMed Web of Science Google Scholar
First citationKleywegt, G. J. & Jones, T. A. (1997). Methods Enzymol. 277, 208–230. CrossRef PubMed CAS Web of Science Google Scholar
First citationKleywegt, G. J. & Jones, T. A. (1998). Acta Cryst. D54, 1119–1131. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationKoparde, V. N., Scarsdale, J. N. & Kellogg, G. E. (2011). PLoS One, 6, e15920. Web of Science CrossRef PubMed Google Scholar
First citationLeontis, N. B. & Westhof, E. (2001). RNA, 7, 499–512. Web of Science CrossRef PubMed CAS Google Scholar
First citationLovell, S. C., Davis, I. W., Arendall, W. B. III, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S. & Richardson, D. C. (2003). Proteins, 50, 437–450. Web of Science CrossRef PubMed CAS Google Scholar
First citationLovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. (2000). Proteins, 40, 389–408. Web of Science CrossRef PubMed CAS Google Scholar
First citationMurshudov, 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. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMurshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240–255. CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationOldfield, T. J. (2001). Acta Cryst. D57, 82–94. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationPettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). J. Comput. Chem. 25, 1605–1612. Web of Science CrossRef PubMed CAS Google Scholar
First citationSaenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag. Google Scholar
First citationSchröder, G. F., Levitt, M. & Brunger, A. T. (2010). Nature (London), 464, 1218–1222. Web of Science PubMed Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSmart, O., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Vonrhein, C., Womack, T. & Bricogne, G. (2008). Abstr. Annu. Meet. Am. Crystallogr. Assoc., Abstract TP139, p. 117. Google Scholar
First citationStorici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. & Schirmer, T. (2004). J. Biol. Chem. 279, 363–373. Web of Science CrossRef PubMed CAS Google Scholar
First citationSussman, J. L., Holbrook, S. R., Church, G. M. & Kim, S.-H. (1977). Acta Cryst. A33, 800–804. CrossRef CAS IUCr Journals Web of Science Google Scholar
First citationTronrud, D. E., Berkholz, D. S. & Karplus, P. A. (2010). Acta Cryst. D66, 834–842. Web of Science CrossRef IUCr Journals Google Scholar
First citationTronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). Acta Cryst. A43, 489–501. CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationUsón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H. J. & Sheldrick, G. M. (1999). Acta Cryst. D55, 1158–1167. Web of Science CrossRef IUCr Journals Google Scholar
First citationVagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F. & Murshudov, G. N. (2004). Acta Cryst. D60, 2184–2195. Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWord, J. M., Bateman, R. C., Presley, B. K., Lovell, S. C. & Richardson, D. C. (2000). Protein Sci. 9, 2251–2259. CrossRef PubMed CAS Google Scholar
First citationWord, J. M., Lovell, S. C., LaBean, T. H., Taylor, H. C., Zalis, M. E., Presley, B. K., Richardson, J. S. & Richardson, D. C. (1999). J. Mol. Biol. 285, 1711–1733. Web of Science CrossRef CAS PubMed Google Scholar
First citationWord, J. M., Lovell, S. C., Richardson, J. S. & Richardson, D. C. (1999). J. Mol. Biol. 285, 1735–1747. Web of Science CrossRef CAS PubMed Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.