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X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c 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 22% PEG4K
10 mM sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.14 α = 90 b = 31.79 β = 90.347 c = 73.74 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 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 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 2.13 28.04 99 0.078 0.086 0.034 0.998 14.5 6.2 13153
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 2.13 2.17 97.3 0.643 0.721 0.318 0.898 2.3 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1jvt 2.13 28.04 13128 674 98.183 0.197 0.1923 0.1982 0.275 0.2787 39.806
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] -0.143 -0.192 -0.072 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_3_deg 15.553 r_dihedral_angle_4_deg 15.093 r_lrange_it 9.283 r_lrange_other 9.28 r_dihedral_angle_1_deg 7.775 r_scangle_it 6.656 r_scangle_other 6.465 r_mcangle_it 6.109 r_mcangle_other 6.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_3_deg 15.553 r_dihedral_angle_4_deg 15.093 r_lrange_it 9.283 r_lrange_other 9.28 r_dihedral_angle_1_deg 7.775 r_scangle_it 6.656 r_scangle_other 6.465 r_mcangle_it 6.109 r_mcangle_other 6.105 r_scbond_it 4.178 r_scbond_other 4.174 r_mcbond_other 3.913 r_mcbond_it 3.912 r_angle_refined_deg 2.195 r_angle_other_deg 1.322 r_nbd_other 0.223 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_other 0.136 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.073 r_xyhbond_nbd_other 0.028 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 1885 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction autoPROC data scaling PHASER phasing