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Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.7 293 CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH
3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG
REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 microL DMSO.
Crystal Properties Matthews coefficient Solvent content 1.79 31.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.957 α = 88.76 b = 31.794 β = 71.99 c = 34.055 γ = 68.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD APEX II CCD CONFOCAL MIRROR OPTICS 2012-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.13 32.21 94.1 0.086 7.2 2.9 35817
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.16 77 0.31 2 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4oxe 1.13 32.21 33282 1762 94.09 0.17964 0.1775 0.1845 0.21982 0.2229 RANDOM 12.268
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_sphericity_free 27.301 r_dihedral_angle_4_deg 19.942 r_sphericity_bonded 11.116 r_dihedral_angle_3_deg 10.158 r_rigid_bond_restr 8.793 r_dihedral_angle_1_deg 6.948 r_scangle_other 4.131 r_long_range_B_refined 3.87 r_long_range_B_other 3.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_sphericity_free 27.301 r_dihedral_angle_4_deg 19.942 r_sphericity_bonded 11.116 r_dihedral_angle_3_deg 10.158 r_rigid_bond_restr 8.793 r_dihedral_angle_1_deg 6.948 r_scangle_other 4.131 r_long_range_B_refined 3.87 r_long_range_B_other 3.869 r_scbond_it 3.526 r_scbond_other 3.523 r_mcangle_other 2.77 r_mcangle_it 2.602 r_mcbond_it 2.096 r_angle_refined_deg 2.056 r_mcbond_other 1.869 r_angle_other_deg 1.044 r_chiral_restr 0.149 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 986 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement SAINT data reduction APEX 2 data scaling PHASER phasing