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X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with human serum albumin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 25-30% PEG3350 -50 mM potassium phosphate buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.07 α = 90 b = 86.55 β = 102.548 c = 59.5 γ = 90
Symmetry Space Group P 1 21 1
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 2020-12-05 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 3.9 47.42 99 0.139 0.986 7.3 3.4 5252
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 3.9 3.97 99.6 0.929 1.097 0.573 0.568 2.5 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.9 47.42 4966 263 93.363 0.293 0.2917 0.2928 0.3275 0.3236 112.871
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] -1.282 1.783 -0.81 1.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.923 r_dihedral_angle_4_deg 18.743 r_lrange_it 17.921 r_lrange_other 17.918 r_dihedral_angle_3_deg 16.189 r_mcangle_other 9.842 r_mcangle_it 9.839 r_scangle_it 9.175 r_scangle_other 9.174 r_dihedral_angle_1_deg 6.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.923 r_dihedral_angle_4_deg 18.743 r_lrange_it 17.921 r_lrange_other 17.918 r_dihedral_angle_3_deg 16.189 r_mcangle_other 9.842 r_mcangle_it 9.839 r_scangle_it 9.175 r_scangle_other 9.174 r_dihedral_angle_1_deg 6.009 r_mcbond_it 5.757 r_mcbond_other 5.733 r_scbond_it 5.218 r_scbond_other 5.218 r_angle_other_deg 1.597 r_angle_refined_deg 1.502 r_symmetry_xyhbond_nbd_refined 0.445 r_nbd_refined 0.275 r_nbd_other 0.228 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.174 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_ext_dist_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4195 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing