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X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with ribonuclease A
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 5.1 293 20% PEG4000, and 0.1 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.04 α = 90 b = 32.64 β = 90.109 c = 73.45 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 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 1.77 73.45 99.7 0.077 0.085 0.035 0.997 12 5.7 23489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 100 0.881 0.966 0.393 0.86 2.4 5.9
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 1.77 73.45 23406 1094 99.254 0.211 0.208 0.2154 0.2761 0.2771 34.929
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] -0.146 -0.075 0.09 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.065 r_dihedral_angle_3_deg 13.381 r_dihedral_angle_4_deg 12.891 r_lrange_it 8.156 r_lrange_other 8.109 r_dihedral_angle_1_deg 7.047 r_scangle_it 6.182 r_scangle_other 5.928 r_mcangle_it 4.275 r_mcangle_other 4.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.065 r_dihedral_angle_3_deg 13.381 r_dihedral_angle_4_deg 12.891 r_lrange_it 8.156 r_lrange_other 8.109 r_dihedral_angle_1_deg 7.047 r_scangle_it 6.182 r_scangle_other 5.928 r_mcangle_it 4.275 r_mcangle_other 4.268 r_scbond_it 3.524 r_scbond_other 3.52 r_mcbond_it 2.78 r_mcbond_other 2.771 r_angle_refined_deg 1.68 r_angle_other_deg 1.42 r_symmetry_xyhbond_nbd_other 0.317 r_nbd_refined 0.25 r_symmetry_xyhbond_nbd_refined 0.243 r_xyhbond_nbd_refined 0.234 r_symmetry_nbd_refined 0.234 r_symmetry_nbd_other 0.204 r_nbd_other 0.191 r_nbtor_refined 0.157 r_ext_dist_refined_d 0.109 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.072 r_metal_ion_refined 0.041 r_gen_planes_refined 0.016 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 1852 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing