Paired refinement and crystal anisotropy

P. Kolenko1,2, P. Mikulecký2, P.N. Pham2, M. Malý1,2, B. Schneider2

1Czech Technical University in Prague, Břehová 7, 115 19 Prague

2Institute of Biotechnology CAS, v.v.i., Průmyslová 595, 252 50 Vestec

petr.kolenko@fjfi.cvut.cz


Anisotropy in diffraction qualities of crystals may represent a serious threat to the structure determination process. When the differences in various directions of the reciprocal space exceed the range of 0.5 Å resolution, problems with phasing may arise, and the structure refinement process is frequently unstable. Such difficulties also appear for structures with high resolution. Although a limited number of tools for the data analysis is available, the current praxis is not standardized and needs thorough revision.

We analyzed diffraction data from a crystal of an engineered protein binder with a promising application as a protein therapeutics [1]. The protein crystallized in space group I4122. The initial diffraction data quality indicators of the data processed the standard way suggested the high-resolution diffraction limit at 2.9 Å. However, a combination of data processed with STARANISO [2] and paired refinement with PAIREF [3] showed a possible extension of the diffraction limit to 2.6 Å in the direction along the l axis. Calculated electron density display moderate improvement and easier interpretation for some side chains.

 

1. P. N. Pham, M. Huličiak, L. Biedermannová, J. Černý, T. Charnavets, G. Fuertes, Š. Herynek, L. Kolářová, P. Kolenko, J. Pavlíček, J. Zahradník, P. Mikulecký, B. Schneider, Viruses, 13, (2021), 190.

2. I. J. Tickle, C. Flensburg, P. Keller, W. Paciorek, A. Sharff, C. Vonrhein, G. Bricogne. (2018). STARANISO (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). Cambridge, United Kingdom: Global Phasing Ltd.

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

This work was supported by MEYS CR (projects CAAS – CZ.02.1.01/0.0/0.0/16_019/0000778) from the ERDF fund and by the GA CTU in Prague (SGS22/114/OHK4/2T/14).