An addendum is published to Tanley et al. [(2014), Acta Cryst. F70, 1135–1142].
Keywords: 4xan re-refinement, raw diffraction data, paired model refinement, electron density assessment, resolution limit assessment, addendum
Abstract
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 ▸) to the critique article of Shabalin et al. (2015 ▸), 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 ▸) article. We have considered the preference of Shabalin et al. (2015 ▸) 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 ▸) is highly unlikely, but nevertheless we still cannot offer an explanation for that shape, confirming our earlier analysis described in Tanley et al. (2014 ▸).
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 ▸). In our accompanying arXiv article (Tanley et al., 2016 ▸) 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 ▸). 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 ▸).
Supplementary Material
PDB reference: re-refinement of 4xan, 5hmj
Supporting Information.. DOI: 10.1107/S2053230X16000777/no5103sup1.pdf
Acknowledgments
We thank Shabalin et al. (2015 ▸) 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
- 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. [DOI] [PMC free article] [PubMed]
- Schreurs, A. M. M., Xian, X. & Kroon-Batenburg, L. M. J. (2010). J. Appl. Cryst. 43, 70–82.
- Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W. & Wlodawer, A. (2015). Acta Cryst. D71, 1965–1979. [DOI] [PMC free article] [PubMed]
- 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. [DOI] [PubMed]
- 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. [DOI] [PMC free article] [PubMed]
- Tanley, S. W. M., Kroon-Batenburg, L. M. J., Schreurs, A. M. M. & Helliwell, J. R. (2016). arXiv:1602.07183.
Associated Data
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Supplementary Materials
PDB reference: re-refinement of 4xan, 5hmj
Supporting Information.. DOI: 10.1107/S2053230X16000777/no5103sup1.pdf