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Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (1 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 3.08 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.142 α = 90 b = 67.142 β = 90 c = 64.791 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 2022-08-24 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 1.54 21.98 100 0.077 0.041 0.998 12.3 4.1 25583
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 1.54 1.56 99.8 2.388 1.763 0.087 0.4 2.6
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 1.54 21.637 25548 1291 99.926 0.197 0.1952 0.2023 0.2222 0.2301 22.596
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 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.742 r_dihedral_angle_3_deg 15.686 r_dihedral_angle_2_deg 8.475 r_lrange_it 7.519 r_lrange_other 7.213 r_dihedral_angle_1_deg 6.632 r_scangle_other 4.983 r_scangle_it 4.893 r_mcangle_it 3.558 r_mcangle_other 3.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.742 r_dihedral_angle_3_deg 15.686 r_dihedral_angle_2_deg 8.475 r_lrange_it 7.519 r_lrange_other 7.213 r_dihedral_angle_1_deg 6.632 r_scangle_other 4.983 r_scangle_it 4.893 r_mcangle_it 3.558 r_mcangle_other 3.556 r_scbond_it 3.237 r_scbond_other 3.23 r_angle_refined_deg 3.198 r_mcbond_it 2.419 r_mcbond_other 2.417 r_angle_other_deg 0.551 r_symmetry_xyhbond_nbd_other 0.346 r_xyhbond_nbd_refined 0.321 r_symmetry_xyhbond_nbd_refined 0.254 r_nbd_refined 0.224 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.181 r_nbd_other 0.173 r_symmetry_nbd_refined 0.165 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing