addenda and errata\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL BIOLOGY
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ISSN: 2053-230X
Volume 72| Part 3| March 2016| Pages 251-252

Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution

aSchool of Chemistry, Faculty of Engineering and Physical Sciences, University of Manchester, Brunswick Street, Manchester, M13 9PL, England, and bCrystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
*Correspondence e-mail: john.helliwell@manchester.ac.uk

Edited by N. Sträter, University of Leipzig, Germany (Received 5 November 2015; accepted 14 January 2016; online 19 February 2016)

A re-refinement of 4xan , hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135–1142] . This follows a previous re-refinement and PDB deposition (4yem ) by Shabalin et al. [(2015), Acta Cryst. D71, 1965–1979 ]. The critical evaluation of the original PDB deposition (4xan ), and the subsequent critical examination of the re-refined structure (4yem ), has led to an improved model (PDB code 5hmj ).

A re-refinement of 4xan , hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made. This follows our response (Tanley et al., 2015[Tanley, S. W. M., Diederichs, K., Kroon-Batenburg, L. M. J., Levy, C., Schreurs, A. M. M. & Helliwell, J. R. (2015). Acta Cryst. D71, 1982-1983.]) to the critique article of Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]), suggesting the need for corrections to some solute molecule interpretations of electron density in 4xan and removal of an organic moiety as a ligand to the platinum ion coordinated to His15. This had been mistakenly included in our PDB file in an attempt by us to model the `shaped' electron density for one coordination site to the Pt bound to the Nδ of His15, which we had rejected, and was not consistent with our Tanley et al. (2014[Tanley, S. W. M., Diederichs, K., Kroon-Batenburg, L. M. J., Levy, C., Schreurs, A. M. M., Helliwell, J. R. & (2014). Acta Cryst. F70, 1135-1142.]) article. We have considered the preference of Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]) to model a chlorine in this density and a close-by bromine at partial occupancy to explain the `shape'. However, as the bromide concentration is in huge excess over chloride (by 20-fold), we think that the 4yem interpretation by Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]) is highly unlikely, but nevertheless we still cannot offer an explanation for that shape, confirming our earlier analysis described in Tanley et al. (2014[Tanley, S. W. M., Diederichs, K., Kroon-Batenburg, L. M. J., Levy, C., Schreurs, A. M. M., Helliwell, J. R. & (2014). Acta Cryst. F70, 1135-1142.]).

The analysis presented here is based on new diffraction data processing to 1.3 Å resolution. The higher resolution limit was evaluated using EVAL (Schreurs et al., 2010[Schreurs, A. M. M., Xian, X. & Kroon-Batenburg, L. M. J. (2010). J. Appl. Cryst. 43, 70-82.]). In our accompanying arXiv article (Tanley et al., 2016[Tanley, S. W. M., Kroon-Batenburg, L. M. J., Schreurs, A. M. M. & Helliwell, J. R. (2016). arXiv:1602.07183.]) we document in detail our different solvent and split occupancy side-chain electron-density interpretations as evidence for our statement of approach in our response article (Tanley et al., 2015[Tanley, S. W. M., Diederichs, K., Kroon-Batenburg, L. M. J., Levy, C., Schreurs, A. M. M. & Helliwell, J. R. (2015). Acta Cryst. D71, 1982-1983.]). Our critical re-examination includes comparisons based on 4xan diffraction data images that have been reprocessed with three different software packages so as to evaluate the possibility of variations in electron-density interpretations resulting from the use of different software. Overall our finalized model (PDB code 5hmj ) (see Table S1 in the Supporting Information) is now improved over 4xan .

The following reference is cited in the Supporting Information for this article: Afonine et al. (2012[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.]).

Supporting information


Acknowledgements

We thank Shabalin et al. (2015[Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965-1979.]) for their valuable critique. We are very grateful to Dr Kay Diederichs for valuable discussions and provision of XDS processed diffraction data to 1.375 Å. We thank Dr Colin Levy for helpful comments on the model refinement methodology. SWMT was funded under an EPSRC PhD Research Studentship at the School of Chemistry, University of Manchester. We acknowledge Diamond Light Source for beamtime on I04 under the University of Manchester monthly beamtime usage.

References

First citationAfonine, 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.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSchreurs, A. M. M., Xian, X. & Kroon-Batenburg, L. M. J. (2010). J. Appl. Cryst. 43, 70–82.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationShabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965–1979.  Web of Science CrossRef IUCr Journals Google Scholar
First citationTanley, S. W. M., Diederichs, K., Kroon-Batenburg, L. M. J., Levy, C., Schreurs, A. M. M. & Helliwell, J. R. (2015). Acta Cryst. D71, 1982–1983.  Web of Science CrossRef IUCr Journals Google Scholar
First citationTanley, S. W. M., Diederichs, K., Kroon-Batenburg, L. M. J., Levy, C., Schreurs, A. M. M., Helliwell, J. R. & (2014). Acta Cryst. F70, 1135–1142.  CrossRef IUCr Journals Google Scholar
First citationTanley, S. W. M., Kroon-Batenburg, L. M. J., Schreurs, A. M. M. & Helliwell, J. R. (2016). arXiv:1602.07183.  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.

Journal logoSTRUCTURAL BIOLOGY
COMMUNICATIONS
ISSN: 2053-230X
Volume 72| Part 3| March 2016| Pages 251-252
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