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Crystal Structure of the ring nuclease Sso2081 Y133F mutant from Saccharolobus solfataricus in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.747 α = 90 b = 95.253 β = 107.803 c = 45.836 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2022-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 50 97.6 0.086 11.6 4.7 24137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 1.183
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 7YHL 2 47.626 24114 1177 99.76 0.226 0.2241 0.2301 0.2556 0.2608 49.345
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] 1.979 1.075 0.663 -2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.335 r_dihedral_angle_3_deg 13.364 r_lrange_other 11.681 r_lrange_it 11.68 r_scangle_it 9.65 r_scangle_other 9.647 r_mcangle_it 6.889 r_mcangle_other 6.887 r_scbond_it 6.798 r_scbond_other 6.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.335 r_dihedral_angle_3_deg 13.364 r_lrange_other 11.681 r_lrange_it 11.68 r_scangle_it 9.65 r_scangle_other 9.647 r_mcangle_it 6.889 r_mcangle_other 6.887 r_scbond_it 6.798 r_scbond_other 6.797 r_dihedral_angle_1_deg 6.701 r_mcbond_it 5.225 r_mcbond_other 5.224 r_dihedral_angle_2_deg 4.703 r_angle_refined_deg 1.6 r_angle_other_deg 0.505 r_symmetry_xyhbond_nbd_refined 0.211 r_nbd_other 0.205 r_symmetry_nbd_other 0.185 r_nbd_refined 0.174 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.161 r_symmetry_nbd_refined 0.13 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.072 r_chiral_restr_other 0.037 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2849 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing PHENIX model building Coot model building HKL-2000 data reduction