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X-ray structure of the adduct formed upon reaction of the five-coordinate Pt(II) complex, 1-Me,Me, with HEWL at pH 7.5
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 7.5 293 2.0 M sodium formate
0.1 M Hepes buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.58 α = 90 b = 78.58 β = 90 c = 37.05 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 PILATUS 6M 2022-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
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 1.25 55.564 99.9 0.046 0.999 22.9 12.7 32632
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 100 1.069 0.854 2.3 12
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 THROUGHOUT 193L 1.25 55.564 32632 1606 99.841 0.184 0.1824 0.1863 0.2179 0.223 19.592
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] -0.073 -0.073 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.453 r_dihedral_angle_4_deg 18.216 r_dihedral_angle_3_deg 16.41 r_dihedral_angle_1_deg 6.395 r_lrange_other 6.154 r_lrange_it 6.151 r_scangle_it 4.631 r_scangle_other 4.628 r_scbond_it 3.06 r_scbond_other 3.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.453 r_dihedral_angle_4_deg 18.216 r_dihedral_angle_3_deg 16.41 r_dihedral_angle_1_deg 6.395 r_lrange_other 6.154 r_lrange_it 6.151 r_scangle_it 4.631 r_scangle_other 4.628 r_scbond_it 3.06 r_scbond_other 3.058 r_angle_refined_deg 2.358 r_mcangle_other 2.054 r_mcangle_it 2.034 r_angle_other_deg 1.638 r_mcbond_it 1.542 r_mcbond_other 1.475 r_nbd_other 0.271 r_symmetry_nbd_refined 0.262 r_nbd_refined 0.234 r_symmetry_nbd_other 0.221 r_xyhbond_nbd_refined 0.214 r_chiral_restr 0.198 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing