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Crystal structure of bovine pancreatic ribonuclease A in complex with [Sp-PS]-mU-dT dinucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 281 22-25 % (w/v) PEG 4000, 20 mM sodium citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.315 α = 90 b = 32.709 β = 90.069 c = 72.802 γ = 90
Symmetry Space Group C 1 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 100 PIXEL RIGAKU HyPix-6000HE 2023-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 17.435 98.8 0.078 0.094 0.051 0.994 9.6 3.1 22015 9.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 95.8 0.243 0.294 0.161 0.93 3.4 2.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 17.435 21996 1122 98.517 0.167 0.1641 0.2303 0.2217 15.904
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] 0.162 0.168 0.075 -0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.987 r_dihedral_angle_3_deg 13.084 r_dihedral_angle_1_deg 6.906 r_lrange_it 6.697 r_lrange_other 6.345 r_dihedral_angle_2_deg 5.82 r_scangle_it 4.053 r_scangle_other 4.052 r_mcangle_it 2.759 r_mcangle_other 2.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.987 r_dihedral_angle_3_deg 13.084 r_dihedral_angle_1_deg 6.906 r_lrange_it 6.697 r_lrange_other 6.345 r_dihedral_angle_2_deg 5.82 r_scangle_it 4.053 r_scangle_other 4.052 r_mcangle_it 2.759 r_mcangle_other 2.759 r_scbond_it 2.387 r_scbond_other 2.384 r_mcbond_it 1.713 r_mcbond_other 1.704 r_angle_refined_deg 1.548 r_angle_other_deg 0.562 r_xyhbond_nbd_refined 0.283 r_nbd_refined 0.219 r_symmetry_nbd_other 0.203 r_nbd_other 0.187 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.091 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.036 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1875 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing