Crystallographic resolution is a key characteristic of diffraction data and represents one of the first decisions an experimenter has to make in data evaluation. Conservative approaches to the high-resolution cutoff determination are based on a number of criteria applied to the processed X-ray diffraction data only. However, high-resolution data that are weaker than arbitrary cutoffs can still result in the improvement of electron-density maps and refined structure models. Therefore, the impact of reflections from resolution shells higher than those previously used in conservative structure refinement should be analysed by the paired refinement protocol. For this purpose, a tool called PAIREF was developed to provide automation of this protocol. As a new feature, a complete cross-validation procedure has also been implemented. Here, the design, usage and control of the program are described, and its application is demonstrated on six data sets. The results prove that the inclusion of high-resolution data beyond the conventional criteria can lead to more accurate structure models.

Faculty of Nuclear Sciences and Physical Engineering Czech Technical University Prague Břehová 7 Prague 11519 Czech Republic

Institute of Biotechnology of the Czech Academy of Sciences Biocev Průmyslová 595 Vestec 25250 Czech Republic

University of Konstanz Box M647 Konstanz 78457 Germany

Zobrazit více v PubMed

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. PubMed PMC

Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352–367. PubMed PMC

Behnen, J., Köster, H., Neudert, G., Craan, T., Heine, A. & Klebe, G. (2012). ChemMedChem 7, 248–261. PubMed

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. PubMed PMC

Brünger, A. T. (1993). Acta Cryst. D49, 24–36. PubMed

DeLano Scientific (2017). The PyMOL Molecular Graphics System, version 2.0. Schrödinger, LLC.

Diederichs, K. & Karplus, P. A. (2013). Acta Cryst. D69, 1215–1222. PubMed PMC

Ding, J., Fraser, M. E., Meyer, J. H., Bartlett, P. A. & James, M. N. G. (1998). J. Am. Chem. Soc. 120, 4610–4621.

Drenth, J. & Jeroen, M. (2010). Principles of Protein X-ray Crystallography, pp. 248–278. New York: Springer.

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. PubMed PMC

Evans, P. R. (2011). Acta Cryst. D67, 282–292. PubMed PMC

Evans, P. R. & Murshudov, G. N. (2013). Acta Cryst. D69, 1204–1214. PubMed PMC

Girard, E., Chantalat, L., Vicat, J. & Kahn, R. (2002). Acta Cryst. D58, 1–9. PubMed

Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 126–136.

Holton, J. M., Classen, S., Frankel, K. A. & Tainer, J. A. (2014). FEBS J. 281, 4046–4060. PubMed PMC

Hunter, J. D. (2007). Comput. Sci. Eng. 9, 90–95.

Huschmann, F. U., Linnik, J., Sparta, K., Ühlein, M., Wang, X., Metz, A., Schiebel, J., Heine, A., Klebe, G., Weiss, M. S. & Mueller, U. (2016). Acta Cryst. F72, 346–355. PubMed PMC

Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100–115. PubMed

Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. (2014). IUCrJ, 1, 213–220. PubMed PMC

Kabsch, W. (2010). Acta Cryst. D66, 125–132. PubMed PMC

Karplus, P. A. & Diederichs, K. (2012). Science, 336, 1030–1033. PubMed PMC

Karplus, P. A. & Diederichs, K. (2015). Curr. Opin. Struct. Biol. 34, 60–68. PubMed PMC

Kleywegt, G. J. & Brünger, A. T. (1996). Structure, 4, 897–904. PubMed

Koval’, T., Švecová, L., Østergaard, L. H., Skalova, T., Dušková, J., Hašek, J., Kolenko, P., Fejfarová, K., Stránský, J., Trundová, M. & Dohnálek, J. (2019). Sci. Rep. 9, 13700. PubMed PMC

Lamzin, V. S. & Wilson, K. S. (1993). Acta Cryst. D49, 129–147. PubMed

Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. (2008). Nat. Protoc. 3, 1171–1179. PubMed PMC

Luebben, J. & Gruene, T. (2015). Proc. Natl Acad. Sci. 112, 8999–9003. PubMed PMC

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. PubMed PMC

McNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. (2011). Acta Cryst. D67, 386–394. PubMed PMC

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. PubMed PMC

Read, R. J., Oeffner, R. D. & McCoy, A. J. (2020). Acta Cryst. D76, 19–27. PubMed PMC

Rossum, G. van (1995). Python Tutorial. Amsterdam: Centrum voor Wiskunde en Informatica.

Sheldrick, G. M. (2002). Z. Kristallogr. 217, 644–650.

Simmons, C. R., Krishnamoorthy, K., Granett, S. L., Schuller, D. J., Dominy, J. E., Begley, T. P., Stipanuk, M. H. & Karplus, P. A. (2008). Biochemistry, 47, 11390–11392. PubMed PMC

Simmons, C. R., Liu, Q., Huang, Q., Hao, Q., Begley, T. P., Karplus, P. A. & Stipanuk, M. H. (2006). J. Biol. Chem. 281, 18723–18733. PubMed

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. PubMed PMC

Tickle, I. (2011). Number of cycles in REFMAC. https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg22423.html.

Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). Acta Cryst. D55, 191–205. PubMed

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235–242. PubMed PMC

Winter, G. (2010). J. Appl. Cryst. 43, 186–190.

Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K. & Evans, G. (2018). Acta Cryst. D74, 85–97. PubMed PMC

Zahradník, J., Kolářová, L., Pařízková, H., Kolenko, P. & Schneider, B. (2018). Fish Shellfish Immunol. 79, 140–152. PubMed

Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia

The CCP4 suite: integrative software for macromolecular crystallography

PAIREF: paired refinement also for Phenix users