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X-ray structure of the adduct formed upon reaction 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 4.5 298 20% ethylene glycol, 0.6 M sodium nitrate and 0.1 sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.4 α = 90 b = 78.4 β = 90 c = 37.15 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 1.6 39.203 99.6 0.07 0.999 25.3 21.6 15767
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 1.6 1.63 99.3 1.2532 0.887 3.2 23.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 39.203 15625 790 98.824 0.186 0.1832 0.2298 0.2488 26.483
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] -0.162 -0.162 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.204 r_dihedral_angle_4_deg 24.442 r_dihedral_angle_3_deg 12.986 r_lrange_it 7.047 r_lrange_other 7.005 r_dihedral_angle_1_deg 6.982 r_scangle_it 5.408 r_scangle_other 5.395 r_scbond_it 3.416 r_scbond_other 3.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.204 r_dihedral_angle_4_deg 24.442 r_dihedral_angle_3_deg 12.986 r_lrange_it 7.047 r_lrange_other 7.005 r_dihedral_angle_1_deg 6.982 r_scangle_it 5.408 r_scangle_other 5.395 r_scbond_it 3.416 r_scbond_other 3.415 r_mcangle_it 3.159 r_mcangle_other 3.137 r_mcbond_it 2.376 r_mcbond_other 2.313 r_angle_refined_deg 1.699 r_angle_other_deg 1.501 r_symmetry_xyhbond_nbd_refined 0.307 r_symmetry_nbd_refined 0.226 r_nbd_other 0.224 r_xyhbond_nbd_refined 0.222 r_nbd_refined 0.22 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.165 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_ext_dist_refined_d 0.004 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 106 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing