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X-ray structure of the adduct formed upon reaction 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 4.5 298 20% ethylene glycol, 0.6 M sodium nitrate and 0.1 sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.57 α = 90 b = 77.57 β = 90 c = 37.64 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 2021-12-04 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 1.36 38.78 100 0.08 0.999 21.3 23.4 25229
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 1.36 1.38 100 2.079 0.782 2.2 24.5
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 1.36 38.78 24654 1189 97.562 0.174 0.1728 0.1824 0.2082 0.2139 20.421
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 30.277 r_dihedral_angle_4_deg 20.518 r_dihedral_angle_3_deg 15.312 r_lrange_it 6.56 r_dihedral_angle_1_deg 6.523 r_lrange_other 6.331 r_scangle_it 4.691 r_scangle_other 4.688 r_scbond_it 3.112 r_scbond_other 3.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.277 r_dihedral_angle_4_deg 20.518 r_dihedral_angle_3_deg 15.312 r_lrange_it 6.56 r_dihedral_angle_1_deg 6.523 r_lrange_other 6.331 r_scangle_it 4.691 r_scangle_other 4.688 r_scbond_it 3.112 r_scbond_other 3.109 r_mcangle_other 2.417 r_mcangle_it 2.414 r_angle_refined_deg 1.877 r_mcbond_it 1.759 r_mcbond_other 1.655 r_angle_other_deg 1.611 r_nbd_other 0.348 r_symmetry_nbd_refined 0.267 r_xyhbond_nbd_refined 0.246 r_nbd_refined 0.236 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.104 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_ext_dist_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing