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X-ray structure of the adduct formed upon reaction of RNase A with [Ru2(D-p-FPhF)(O2CCH3)2(O2CO)] complex
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 buffer at pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.54 α = 90 b = 32.6 β = 90.014 c = 72.35 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 2022-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 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 1.74 50.27 94.4 0.052 0.997 11.6 2.9 23214
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 1.74 1.77 0.466 0.745 2.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.74 50.27 22932 1160 93.486 0.195 0.1922 0.1992 0.26 0.2625 0.261 25.606
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] -0.082 0.147 0.084 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.896 r_dihedral_angle_3_deg 11.689 r_lrange_it 7.35 r_lrange_other 7.122 r_dihedral_angle_1_deg 7.117 r_dihedral_angle_2_deg 5.718 r_scangle_it 4.56 r_scangle_other 4.557 r_mcangle_it 4.003 r_mcangle_other 4.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.896 r_dihedral_angle_3_deg 11.689 r_lrange_it 7.35 r_lrange_other 7.122 r_dihedral_angle_1_deg 7.117 r_dihedral_angle_2_deg 5.718 r_scangle_it 4.56 r_scangle_other 4.557 r_mcangle_it 4.003 r_mcangle_other 4.002 r_scbond_it 2.933 r_scbond_other 2.827 r_mcbond_it 2.641 r_mcbond_other 2.641 r_angle_refined_deg 1.581 r_angle_other_deg 0.552 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.197 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.173 r_nbd_other 0.17 r_xyhbond_nbd_other 0.125 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1898 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing