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Room temperature X-ray diffraction studies of cisplatin binding to HEWL in DMSO media after 14 months of crystal storage - new refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.7 295 HEWL co-crystallized with cisplatin with 5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7
Crystal Properties Matthews coefficient Solvent content 2.07 40.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.113 α = 90 b = 79.113 β = 90 c = 37.985 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD APEX II CCD 2012-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2 50 100 0.086 0.086 0.092 0.032 8.8 7.9 8602 8602 -3 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.571 0.63 0.264 0.865 2.7 5.6 411
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 FOURIER SYNTHESIS THROUGHOUT 4G4A 2 50 8107 450 99.8 0.1481 0.1464 0.1561 0.1788 0.1813 RANDOM 28.046
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.32 r_sphericity_bonded 30.527 r_sphericity_free 25.995 r_dihedral_angle_4_deg 23.506 r_dihedral_angle_3_deg 14.34 r_dihedral_angle_1_deg 6.307 r_angle_refined_deg 1.578 r_mcangle_it 1.54 r_angle_other_deg 1.069 r_mcbond_it 0.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.32 r_sphericity_bonded 30.527 r_sphericity_free 25.995 r_dihedral_angle_4_deg 23.506 r_dihedral_angle_3_deg 14.34 r_dihedral_angle_1_deg 6.307 r_angle_refined_deg 1.578 r_mcangle_it 1.54 r_angle_other_deg 1.069 r_mcbond_it 0.906 r_mcbond_other 0.905 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 995 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement APEX data collection HKL-3000 data reduction HKL-3000 data scaling Coot model building PDB_EXTRACT data extraction PHASER phasing