Carboplatin binding to a model protein in non-NaCl conditions to eliminate partial conversion to cisplatin, and the use of different criteria to choose the resolution limit

Hen egg white lysozyme (HEWL) co-crystallisation conditions of carboplatin without sodium chloride (NaCl) have been utilised to eliminate partial conversion of carboplatin to cisplatin observed previously. Tetragonal HEWL crystals were successfully obtained in 65% MPD with 0.1M citric acid buffer at pH 4.0 including DMSO. The X-ray diffraction data resolution to be used for the model refinement was reviewed using several topical criteria together. The CC1/2 criterion implemented in XDS led to data being significant to 2.0{\AA}, compared to the data only being able to be processed to 3.0{\AA} using the Bruker software package (SAINT). Then using paired protein model refinements and DPI values based on the FreeR value, the resolution limit was fine tuned to be 2.3{\AA}. Interestingly this was compared with results from the EVAL software package which gave a resolution limit of 2.2{\AA} solely using crossing 2, but 2.8{\AA} based on the Rmerge values (60%). The structural results showed that carboplatin bound to only the N{\delta} binding site of His-15 one week after crystal growth, whereas five weeks after crystal growth, two molecules of carboplatin are bound to the His-15 residue. In summary several new results have emerged: - firstly non-NaCl conditions showed a carboplatin molecule bound to His-15 of HEWL; secondly binding of one molecule of carboplatin was seen after one week of crystal growth and two molecules were bound after five weeks of crystal growth; and thirdly the use of several criteria to determine the diffraction resolution limit led to the successful use of data to higher resolution.Comment: 14 pages; submitted to Acta Cryst D Biological Crystallography reference number tz504

Погляд на архіви

The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish

Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect

Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses.Comment: 10 pages. One figure with two stereos and two further separate (identical to the stereos) figures with atom labels. This arXiv article is the first part of a Data Revie

Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect

Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses

Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect

Following the interest of L Messori and A Merlino 2016 Coordination Chemistry Reviews in the platinum ions coordination geometries in our PDB entries 4dd4 and 4dd6 we have extended our original analyses

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

A re-refinement of 4xan, hen egg white lysozyme (HEWL) with carboplatin crystallised in NaBr solution, has been made (Tanley et al 2016). This follows our Response article (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. We note Shabalin et al (2015) model of a chlorine in that 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 Shabalin et al 2015 interpretation highly unlikely, but nevertheless we still cannot offer an explanation for that shape, confirming our earlier analysis described in Tanley et al (2014). Following Shabalin et al (2015) reprocessing of the raw diffraction data for 4g4a, we also redid the diffraction data processing for 4xan to a higher resolution using EVAL (Schreurs et al 2010) concluding in favour of 1.3 Angstrom as the resolution limit and which is the basis for our revised PDB file for 4xan (5HMJ). It is very interesting that there is extra X-ray diffraction data from 1.47 to 1.30 Angstrom resolution e.g. with =0.39 and CC1/2 = 0.181 in the final shell (1.30 to 1.322 Angstrom). In this arXiv article 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 the 4xan diffraction data images reprocessing with three different software packages so as to evaluate the possibility of variations in electron density interpretations due to that. Overall our finalised model (PDB code 5HMJ) is now improved over 4xan