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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 4.0
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 pH 4.0
0.6 M sodium Nitrate
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.5 α = 90 b = 77.5 β = 90 c = 37.58 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 1.33 54.801 100 0.038 1 30.3 13 27087
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 1.33 1.35 100 1.251 0.812 2 12.7
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 1.33 54.801 26864 1340 99.967 0.187 0.1854 0.1883 0.2188 0.2153 23.908
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] -0.011 -0.011 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.808 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 14.322 r_lrange_it 6.787 r_dihedral_angle_1_deg 6.439 r_lrange_other 6.115 r_scangle_it 4.753 r_scangle_other 4.395 r_scbond_it 3.932 r_scbond_other 2.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.808 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 14.322 r_lrange_it 6.787 r_dihedral_angle_1_deg 6.439 r_lrange_other 6.115 r_scangle_it 4.753 r_scangle_other 4.395 r_scbond_it 3.932 r_scbond_other 2.864 r_mcangle_it 2.646 r_mcangle_other 2.646 r_mcbond_it 1.896 r_mcbond_other 1.883 r_angle_refined_deg 1.763 r_angle_other_deg 1.545 r_symmetry_nbd_refined 0.279 r_symmetry_xyhbond_nbd_refined 0.273 r_xyhbond_nbd_refined 0.239 r_nbd_refined 0.224 r_nbd_other 0.213 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.173 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 997 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing