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Cross-linked crystal of dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (high 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 3.14 60.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.278 α = 90 b = 67.278 β = 90 c = 65.899 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 273 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 1.6 22.02 99.9 0.079 0.079 0.994 6.9 1.8 23142
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 1.6 1.63 99.2 1.062 1.062 0.339 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 1.6 22.02 23142 1164 99.836 0.183 0.1823 0.1907 0.2015 0.2013 21.27
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] 0.038 0.019 0.038 -0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.613 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_2_deg 8.997 r_lrange_it 7.776 r_lrange_other 7.237 r_dihedral_angle_1_deg 6.395 r_scangle_other 4.489 r_scangle_it 4.484 r_mcangle_it 3.698 r_mcangle_other 3.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.613 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_2_deg 8.997 r_lrange_it 7.776 r_lrange_other 7.237 r_dihedral_angle_1_deg 6.395 r_scangle_other 4.489 r_scangle_it 4.484 r_mcangle_it 3.698 r_mcangle_other 3.696 r_angle_refined_deg 3.219 r_scbond_it 3.013 r_scbond_other 2.979 r_mcbond_other 2.43 r_mcbond_it 2.427 r_angle_other_deg 0.542 r_symmetry_nbd_refined 0.352 r_nbd_other 0.239 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.201 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.165 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 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 127 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing