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Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO.
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, BATCH, TEMPERATURE 295K
Crystal Properties Matthews coefficient Solvent content 2.08 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.1443 α = 90 b = 79.1443 β = 90 c = 37.9968 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 300 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 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.699 35.39 99.68 0.048 0.998 9.8 6.7 13804 18.9861835344
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 1.699 1.728 93.86 2.428 0.56 4.5
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 FREE R-VALUE 4g4a 1.7 35.39 13507 703 97.8626286046 0.182 0.18 0.1826 0.224 0.2255 Random 25.3947691261
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 f_dihedral_angle_d 13.4617637632 f_angle_d 1.29563511294 f_chiral_restr 0.0539763548156 f_bond_d 0.0129972125866 f_plane_restr 0.00685649835475
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement PHASER phasing