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X-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 298 22% PEG4000, 0.1 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.92 α = 90 b = 32.88 β = 90.308 c = 74 γ = 90
Symmetry Space Group C 1 2 1
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 1.76 28.83 98.3 0.097 0.996 10 6.2 24352
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 1.76 1.81 98.3 0.792 0.792 1.7 6.2
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 1.76 28.83 24352 1173 99.311 0.199 0.1976 0.2075 0.2346 0.2435 28.539
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] -0.07 0.143 -0.048 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.38 r_dihedral_angle_3_deg 14.286 r_dihedral_angle_4_deg 11.004 r_lrange_it 7.08 r_dihedral_angle_1_deg 7.07 r_lrange_other 7.023 r_scangle_it 5.487 r_scangle_other 5.481 r_mcangle_it 3.639 r_mcangle_other 3.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.38 r_dihedral_angle_3_deg 14.286 r_dihedral_angle_4_deg 11.004 r_lrange_it 7.08 r_dihedral_angle_1_deg 7.07 r_lrange_other 7.023 r_scangle_it 5.487 r_scangle_other 5.481 r_mcangle_it 3.639 r_mcangle_other 3.629 r_scbond_it 3.557 r_scbond_other 3.556 r_mcbond_it 2.428 r_mcbond_other 2.428 r_angle_refined_deg 1.605 r_angle_other_deg 1.405 r_metal_ion_refined 0.593 r_symmetry_xyhbond_nbd_refined 0.463 r_symmetry_nbd_refined 0.33 r_nbd_other 0.268 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.157 r_ext_dist_refined_d 0.092 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_gen_planes_refined 0.014 r_bond_refined_d 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 1824 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing