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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 60.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.129 α = 90 b = 67.129 β = 90 c = 64.979 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 1.5 21.97 100 0.074 0.022 0.999 22.6 11.1 27554
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 1.53 100 2.144 0.875 0.325 0.9
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 21.97 27520 1379 99.949 0.182 0.1804 0.1886 0.2151 0.2217 20.74
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] -0.001 -0.001 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.111 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_2_deg 8.411 r_lrange_it 6.995 r_dihedral_angle_1_deg 6.734 r_lrange_other 6.541 r_scangle_other 5.007 r_scangle_it 4.916 r_mcangle_it 3.433 r_mcangle_other 3.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.111 r_dihedral_angle_3_deg 14.932 r_dihedral_angle_2_deg 8.411 r_lrange_it 6.995 r_dihedral_angle_1_deg 6.734 r_lrange_other 6.541 r_scangle_other 5.007 r_scangle_it 4.916 r_mcangle_it 3.433 r_mcangle_other 3.431 r_angle_refined_deg 3.227 r_scbond_other 3.221 r_scbond_it 3.177 r_mcbond_it 2.3 r_mcbond_other 2.298 r_angle_other_deg 0.599 r_xyhbond_nbd_refined 0.3 r_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.18 r_nbd_other 0.162 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 170 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing