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X-structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with lysozyme (structure C)
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 and 0.1 Hepes buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.01 α = 90 b = 79.01 β = 90 c = 35.43 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 1.00 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 2.25 39.51 99.8 0.104 0.108 0.026 0.998 19.4 18.2 5691
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 2.25 2.28 98 0.5 0.516 0.123 0.939 9.6 9.6
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 2.25 39.51 5637 262 99.121 0.227 0.2242 0.2295 0.2771 0.2744 56.585
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] -0.039 -0.039 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_4_deg 21.057 r_dihedral_angle_3_deg 17.404 r_lrange_other 10.762 r_lrange_it 10.759 r_scangle_it 8.968 r_scangle_other 8.094 r_dihedral_angle_1_deg 8.019 r_mcangle_it 6.006 r_mcangle_other 5.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_4_deg 21.057 r_dihedral_angle_3_deg 17.404 r_lrange_other 10.762 r_lrange_it 10.759 r_scangle_it 8.968 r_scangle_other 8.094 r_dihedral_angle_1_deg 8.019 r_mcangle_it 6.006 r_mcangle_other 5.977 r_scbond_it 4.887 r_scbond_other 4.877 r_mcbond_it 4.226 r_mcbond_other 4.207 r_angle_refined_deg 1.538 r_angle_other_deg 1.316 r_nbd_refined 0.215 r_symmetry_nbd_other 0.212 r_nbd_other 0.211 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbd_refined 0.112 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_ext_dist_refined_d 0.032 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 995 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing