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Cross-linked crystal of Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (low temperature data collection)
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 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.389 α = 90 b = 67.389 β = 90 c = 64.42 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 2022-07-01 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 22.06 99.3 0.056 0.056 0.998 17.4 1.9 27241
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 97.6 1.296 1.296 0.199 0.6 1.8
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 22.06 27240 1393 99.029 0.187 0.1845 0.1941 0.2244 0.2304 19.63
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] 0.014 0.007 0.014 -0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.437 r_dihedral_angle_3_deg 14.092 r_lrange_it 7.272 r_dihedral_angle_2_deg 6.78 r_dihedral_angle_1_deg 6.72 r_lrange_other 6.545 r_scangle_other 4.088 r_scangle_it 4.066 r_angle_refined_deg 3.304 r_mcangle_it 3.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.437 r_dihedral_angle_3_deg 14.092 r_lrange_it 7.272 r_dihedral_angle_2_deg 6.78 r_dihedral_angle_1_deg 6.72 r_lrange_other 6.545 r_scangle_other 4.088 r_scangle_it 4.066 r_angle_refined_deg 3.304 r_mcangle_it 3.025 r_mcangle_other 3.024 r_scbond_it 2.603 r_scbond_other 2.574 r_mcbond_it 2.04 r_mcbond_other 2.038 r_angle_other_deg 0.546 r_nbd_other 0.253 r_symmetry_xyhbond_nbd_refined 0.235 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.212 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.175 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.01 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 192 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing