Computational protocol: Carboplatin binding to histidine

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[…] Crystals were each scooped into a loop using silicone oil as a cryoprotectant. All X-ray diffraction (XRD) data were measured on a Bruker APEX II home-source diffractometer at an X-ray wavelength of 1.5418 Å, except for one of the NaBr-grown crystals, from which XRD data were collected on beamline I04 at Diamond Light Source (DLS) with an X-ray wavelength of 0.9163 Å; namely, the short-wavelength side of the Br K edge. The XRD data collections were carried out at fixed temperatures between 100 and 127 K (Table 1). For the home laboratory runs the XRD data from each crystal were processed using the Bruker software package SAINT (Bruker AXS, Madison, WI, USA), with the exception of the crystal from the 65% MPD with 0.1 M citric acid buffer at pH 4.0 crystallization mixture, for which one data set was processed with EVAL (Schreurs et al., 2010) and the other with XDS (Kabsch, 2010). The data for the NaBr-grown crystal XRD data set collected on beamline I04 at DLS were processed with MOSFLM (Leslie, 1999).The crystal structures were solved using molecular replacement with Phaser (McCoy et al., 2007), using the reported lysozyme structure with PDB code 2w1y as a molecular search model (Cianci et al., 2008) and restrained refinement with REFMAC5 (Murshudov et al., 2011) from CCP4 (Winn et al., 2011). For the NaBr-grown crystal for which data were collected on beamline I04 at DLS, anisotropic atomic B factors were refined, as the high resolution afforded this possibility, whereas all other data sets were refined with isotropic atomic B factors. Model building, adjustment and refinement were carried out using Coot (Emsley et al., 2010) and REFMAC5 in CCP4. Ligand-binding occupancies were refined using SHELXTL (Sheldrick, 2008). The crystallographic and molecular model-refinement parameters are summarized in Table 1. The e.s.d. values for the Pt occupancies (Table 2) were refined using the full-matrix inversion technique in SHELXL (Sheldrick, 2008). For resolutions worse than 2.5 Å refined occupancy estimates become questionable. Figs. 2, 3, 4, S1 and S2 were prepared with CCP4mg (McNicholas et al., 2011). […]


Carboplatin binding to histidine

2014 Acta Crystallographica. Section F, Structural Biology Communications
PMCID: 4157408
PMID: 25195881
DOI: 10.1107/S2053230X14016161

Pipeline specifications

Software tools REFMAC5, SHELX, CCP4mg
Applications Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma
Diseases Neoplasms
Chemicals Bromine, Carbon, Cisplatin, Platinum, Sodium Chloride, Carboplatin