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X-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure C)
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 4.5 298 22% PEG4000, 0.1 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.75 α = 90 b = 32.69 β = 90.463 c = 73.54 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 1.99 50.424 99.8 0.161 0.988 7.3 5.9 16745
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 1.99 2.08 99.8 0.161 0.638 2.1 5.8
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 1.99 50.424 16617 755 98.641 0.193 0.1909 0.1973 0.2426 0.2492 32.756
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] 0.101 0.134 0.077 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.643 r_dihedral_angle_3_deg 16.71 r_dihedral_angle_4_deg 9.212 r_lrange_it 7.712 r_lrange_other 7.639 r_dihedral_angle_1_deg 7.571 r_scangle_it 4.802 r_scangle_other 4.687 r_mcangle_other 4.262 r_mcangle_it 4.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.643 r_dihedral_angle_3_deg 16.71 r_dihedral_angle_4_deg 9.212 r_lrange_it 7.712 r_lrange_other 7.639 r_dihedral_angle_1_deg 7.571 r_scangle_it 4.802 r_scangle_other 4.687 r_mcangle_other 4.262 r_mcangle_it 4.259 r_scbond_it 2.98 r_scbond_other 2.978 r_mcbond_other 2.736 r_mcbond_it 2.735 r_angle_refined_deg 1.536 r_angle_other_deg 1.367 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_refined 0.224 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.178 r_nbtor_refined 0.16 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.063 r_ext_dist_refined_d 0.013 r_symmetry_xyhbond_nbd_other 0.013 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing