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Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with free phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.1 M Sodium acetate trihydrate, pH 4.5, 25% w/v Polyethylene glycol 1500
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.027 α = 90 b = 38.376 β = 106.412 c = 69.798 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 100 PIXEL DECTRIS EIGER2 S 9M 2022-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97919 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 40.95 95.55 0.067 0.998 10.9 5.29 9099
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.79 95.55 0.748 0.805 1.5 5.32
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 SAD THROUGHOUT 2.7 40.95 9098 483 93.862 0.264 0.2631 0.2571 0.2877 0.2843 117.165
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] 2.966 2.857 -2.26 -2.036
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 28.921 r_lrange_other 28.921 r_scangle_other 19.069 r_scangle_it 19.041 r_mcangle_it 18.559 r_mcangle_other 18.553 r_dihedral_angle_3_deg 16.973 r_dihedral_angle_6_deg 15.479 r_mcbond_it 12.983 r_mcbond_other 12.98
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 28.921 r_lrange_other 28.921 r_scangle_other 19.069 r_scangle_it 19.041 r_mcangle_it 18.559 r_mcangle_other 18.553 r_dihedral_angle_3_deg 16.973 r_dihedral_angle_6_deg 15.479 r_mcbond_it 12.983 r_mcbond_other 12.98 r_scbond_it 12.966 r_scbond_other 12.931 r_dihedral_angle_1_deg 9.505 r_dihedral_angle_2_deg 7.48 r_angle_refined_deg 1.802 r_angle_other_deg 0.633 r_nbd_other 0.257 r_symmetry_nbd_other 0.218 r_xyhbond_nbd_refined 0.191 r_nbd_refined 0.188 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.16 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.029 r_bond_other_d 0.018 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2697 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data scaling MOLREP phasing PHENIX model building Coot model building XDS data reduction