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X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 20% ethylene glycol
0.1 M sodium acetate buffer pH 4.0
0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.2 α = 90 b = 77.2 β = 90 c = 38.53 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 PIXEL DECTRIS PILATUS3 6M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.22 34.52 100 0.056 0.057 0.012 1 24.5 23.2 35283
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 1.22 1.24 100 1.531 1.564 0.315 0.861 2.2 24.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 193L 1.22 34.52 33997 1687 96.489 0.135 0.1328 0.1375 0.1741 0.1735 20.279
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] 0.52 0.52 -1.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.553 r_dihedral_angle_4_deg 23.768 r_dihedral_angle_3_deg 13.024 r_rigid_bond_restr 8.909 r_dihedral_angle_1_deg 6.312 r_lrange_it 5.46 r_lrange_other 5.458 r_scangle_it 4.847 r_scangle_other 4.844 r_scbond_it 4.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.553 r_dihedral_angle_4_deg 23.768 r_dihedral_angle_3_deg 13.024 r_rigid_bond_restr 8.909 r_dihedral_angle_1_deg 6.312 r_lrange_it 5.46 r_lrange_other 5.458 r_scangle_it 4.847 r_scangle_other 4.844 r_scbond_it 4.492 r_scbond_other 4.488 r_angle_refined_deg 2.273 r_mcangle_other 2.217 r_mcangle_it 2.215 r_angle_other_deg 1.917 r_mcbond_it 1.788 r_mcbond_other 1.734 r_symmetry_nbd_refined 0.268 r_xyhbond_nbd_refined 0.253 r_nbd_other 0.246 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.178 r_chiral_restr 0.14 r_symmetry_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.058 r_ext_dist_refined_d 0.041 r_bond_refined_d 0.02 r_metal_ion_refined 0.02 r_bond_other_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction autoPROC data scaling PHASER phasing