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X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) Compound with a S,O Bidentate Ligand (9a=Chloro-(1-(3'-hydroxy)-3-(methylthio)-3-thioxo-prop-1-en-1-olate-O,S)-(dimethylsulfoxide-S)-platinum(II))
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 20 % ethylene glycol, 0.1 M sodium acetate pH 4.5, 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.99 38.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.364 α = 90 b = 78.364 β = 90 c = 37.069 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 100 CCD RIGAKU SATURN 944+ 2014-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.89 99 99.9 0.099 13.8 6 9726
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 4JVT 1.89 55.41 9226 467 99.92 0.16616 0.16331 0.1734 0.21921 0.231 RANDOM 22.62
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] -0.09 -0.09 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.149 r_dihedral_angle_4_deg 20.022 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 6.602 r_long_range_B_refined 6.222 r_long_range_B_other 6.22 r_scangle_other 4.354 r_scbond_it 2.941 r_scbond_other 2.884 r_mcangle_it 2.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.149 r_dihedral_angle_4_deg 20.022 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 6.602 r_long_range_B_refined 6.222 r_long_range_B_other 6.22 r_scangle_other 4.354 r_scbond_it 2.941 r_scbond_other 2.884 r_mcangle_it 2.563 r_mcangle_other 2.561 r_angle_refined_deg 1.837 r_mcbond_it 1.783 r_mcbond_other 1.782 r_angle_other_deg 0.971 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing