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X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) Complex with S,O Bidentate Ligands (9b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J4T
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 1.97 37.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.261 α = 90 b = 78.261 β = 90 c = 36.878 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+ 2014-11-17 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 2.15 55.34 97.9 0.135 11 6.7 43330 6498
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 2.15 2.2 99.2 0.44 2.9 6.6
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 4j4t 2.15 55.34 6177 303 98.08 0.16354 0.16032 0.1728 0.23267 0.2368 RANDOM 28.707
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.171 r_dihedral_angle_4_deg 20.22 r_dihedral_angle_3_deg 13.838 r_dihedral_angle_1_deg 6.789 r_long_range_B_refined 6.656 r_long_range_B_other 6.655 r_scangle_other 4.604 r_mcangle_it 2.936 r_mcangle_other 2.934 r_scbond_it 2.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.171 r_dihedral_angle_4_deg 20.22 r_dihedral_angle_3_deg 13.838 r_dihedral_angle_1_deg 6.789 r_long_range_B_refined 6.656 r_long_range_B_other 6.655 r_scangle_other 4.604 r_mcangle_it 2.936 r_mcangle_other 2.934 r_scbond_it 2.924 r_scbond_other 2.918 r_mcbond_other 1.943 r_mcbond_it 1.942 r_angle_refined_deg 1.793 r_angle_other_deg 0.995 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 100 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing