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X-ray structure of the adduct obtained upon reaction of [Rh2(OCOCH3)(OCOCF3)3] with RNase A (2)
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 0.01 M sodium cintrate buffer pH 5.1
22% PEG4K
Crystal Properties Matthews coefficient Solvent content 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.57 α = 90 b = 32.57 β = 90.461 c = 72.51 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 2021-05-22 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) 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 1.71 30.99 99.9 0.079 0.052 0.997 12.5 6.3 25642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 100 0.795 0.521 0.782 2.2 6.2
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 1.71 30.99 25642 1294 99.864 0.185 0.1827 0.1828 0.2356 0.2356 26.885
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] -0.009 0.027 0.002 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.839 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_4_deg 12.815 r_dihedral_angle_1_deg 7.104 r_lrange_it 6.931 r_lrange_other 6.725 r_scangle_it 4.675 r_scangle_other 4.568 r_mcangle_it 3.66 r_mcangle_other 3.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.839 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_4_deg 12.815 r_dihedral_angle_1_deg 7.104 r_lrange_it 6.931 r_lrange_other 6.725 r_scangle_it 4.675 r_scangle_other 4.568 r_mcangle_it 3.66 r_mcangle_other 3.659 r_scbond_it 3.011 r_scbond_other 2.976 r_mcbond_it 2.44 r_mcbond_other 2.439 r_angle_refined_deg 2.22 r_angle_other_deg 1.448 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.203 r_nbd_other 0.196 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.162 r_symmetry_nbd_refined 0.141 r_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 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 1902 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing