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X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with lysozyme (structure A)
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 4.5 293 1.1 M sodium chloride
0.1 M sodium acetate buffer pH 4.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.4 α = 90 b = 78.4 β = 90 c = 36.92 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 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 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 1.96 55.44 98.6 0.067 0.069 0.015 0.999 29.9 20.9 8548
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 1.96 2 93.4 0.966 0.987 0.204 0.969 4.1 23.3
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 1.96 55.437 8536 412 98.205 0.209 0.2057 0.2146 0.2691 0.2727 40.371
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] -0.197 -0.197 0.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.289 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 15.908 r_lrange_other 10.347 r_lrange_it 10.344 r_scangle_it 7.561 r_scangle_other 7.448 r_dihedral_angle_1_deg 7.381 r_mcangle_other 5.597 r_mcangle_it 5.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.289 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 15.908 r_lrange_other 10.347 r_lrange_it 10.344 r_scangle_it 7.561 r_scangle_other 7.448 r_dihedral_angle_1_deg 7.381 r_mcangle_other 5.597 r_mcangle_it 5.538 r_scbond_it 4.545 r_scbond_other 4.543 r_mcbond_it 4 r_mcbond_other 3.877 r_angle_refined_deg 1.76 r_angle_other_deg 1.412 r_symmetry_nbd_refined 0.28 r_nbd_other 0.268 r_nbd_refined 0.207 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_ext_dist_refined_d 0.011 r_gen_planes_refined 0.009 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 72 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing