In macromolecular crystallography, paired refinement is generally accepted to be the optimal approach for the determination of the high-resolution cutoff. The software tool PAIREF provides automation of the protocol and associated analysis. Support for phenix.refine as a refinement engine has recently been implemented in the program. This feature is presented here using previously published data for thermolysin. The results demonstrate the importance of the complete cross-validation procedure to obtain a thorough and unbiased insight into the quality of high-resolution data.

Faculty of Nuclear Sciences and Physical Engineering Czech Technical University Prague Břehová 7 115 19 Prague 1 Czech Republic

Institute of Biotechnology of the Czech Academy of Sciences BIOCEV Průmyslová 595 252 50 Vestec Czech Republic

University of Konstanz Box M647 78457 Konstanz Germany

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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

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

Campeotto, I., Lebedev, A., Schreurs, A. M. M., Kroon-Batenburg, L. M. J., Lowe, E., Phillips, S. E. V., Murshudov, G. N. & Pearson, A. R. (2018). Sci. Rep. 8, 14876. PubMed PMC

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

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

Headd, J. J., Echols, N., Afonine, P. V., Grosse-Kunstleve, R. W., Chen, V. B., Moriarty, N. W., Richardson, D. C., Richardson, J. S. & Adams, P. D. (2012). Acta Cryst. D68, 381–390. PubMed PMC

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

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

Kovalevskiy, O., Nicholls, R. A., Long, F., Carlon, A. & Murshudov, G. N. (2018). Acta Cryst. D74, 215–227. PubMed PMC

Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., Terwilliger, T. C., Urzhumtsev, A. G., Videau, L. L., Williams, C. J. & Adams, P. D. (2019). Acta Cryst. D75, 861–877.

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

Malý, M., Diederichs, K., Dohnálek, J. & Kolenko, P. (2020). IUCrJ, 7, 681–692. 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

Shabalin, I. G., Porebski, P. J. & Minor, W. (2018). Crystallogr. Rev. 24, 236–262. PubMed PMC

Švecová, L., Østergaard, L. H., Skálová, T., Schnorr, K. M., Koval’, T., Kolenko, P., Stránský, J., Sedlák, D., Dušková, J., Trundová, M., Hašek, J. & Dohnálek, J. (2021). Acta Cryst. D77, 755–775. PubMed PMC

Weichenberger, C. X., Afonine, P. V., Kantardjieff, K. & Rupp, B. (2015). Acta Cryst. D71, 1023–1038. 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

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

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia