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Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (6 h soaking)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 2.5 M NaCl
3.3 M HCOONa
0.1 M Acetate buffer
Crystal Properties Matthews coefficient Solvent content 3.05 59.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.795 α = 90 b = 66.795 β = 90 c = 64.904 γ = 120
Symmetry Space Group P 32 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 93 PIXEL RIGAKU HyPix-6000HE 2022-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.5406
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 1.5 21.86 100 0.079 0.028 0.999 20 8.5 27269
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 1.5 1.53 99.8 2.022 0.975 0.223 0.8 5.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 21.601 27239 1367 99.941 0.18 0.1785 0.1858 0.2157 0.2185 18.86
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] -0.004 -0.002 -0.004 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.429 r_dihedral_angle_3_deg 13.826 r_dihedral_angle_2_deg 8.164 r_lrange_it 7.303 r_dihedral_angle_1_deg 6.778 r_lrange_other 6.658 r_scangle_other 4.155 r_scangle_it 4.153 r_mcangle_it 3.539 r_mcangle_other 3.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.429 r_dihedral_angle_3_deg 13.826 r_dihedral_angle_2_deg 8.164 r_lrange_it 7.303 r_dihedral_angle_1_deg 6.778 r_lrange_other 6.658 r_scangle_other 4.155 r_scangle_it 4.153 r_mcangle_it 3.539 r_mcangle_other 3.537 r_angle_refined_deg 3.359 r_scbond_it 2.738 r_scbond_other 2.733 r_mcbond_other 2.367 r_mcbond_it 2.365 r_angle_other_deg 0.582 r_xyhbond_nbd_refined 0.301 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.216 r_symmetry_nbd_other 0.198 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.181 r_nbd_other 0.161 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing