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X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with lysozyme (structure B)
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 7 293 0.8 M succinic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.15 α = 90 b = 79.15 β = 90 c = 36.03 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 1.48 39.606 99.9 0.075 0.077 0.017 0.999 19.6 19.4 19656
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.51 100 1.616 1.658 0.914 2.3 20.3
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 1.48 39.606 18409 896 93.608 0.227 0.2251 0.233 0.2588 0.2602 26.239
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] -0.236 -0.236 0.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.075 r_dihedral_angle_4_deg 20.155 r_dihedral_angle_3_deg 17.616 r_dihedral_angle_1_deg 7.272 r_lrange_it 6.613 r_lrange_other 6.542 r_scangle_it 4.818 r_scangle_other 4.663 r_mcangle_other 3.018 r_mcangle_it 3.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.075 r_dihedral_angle_4_deg 20.155 r_dihedral_angle_3_deg 17.616 r_dihedral_angle_1_deg 7.272 r_lrange_it 6.613 r_lrange_other 6.542 r_scangle_it 4.818 r_scangle_other 4.663 r_mcangle_other 3.018 r_mcangle_it 3.014 r_scbond_it 2.884 r_scbond_other 2.881 r_mcbond_it 2.219 r_mcbond_other 2.206 r_angle_refined_deg 1.657 r_angle_other_deg 1.461 r_symmetry_xyhbond_nbd_refined 0.269 r_xyhbond_nbd_refined 0.26 r_nbd_refined 0.21 r_symmetry_nbd_other 0.203 r_nbd_other 0.182 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.141 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.084 r_ext_dist_refined_d 0.013 r_bond_refined_d 0.01 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 122 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing