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Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediate
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 0.1 M Sodium acetate trihydrate, pH 5.0, 20% w/v Polyethylene glycol 1500
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.51 α = 90 b = 39.144 β = 105.178 c = 74.088 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 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978 SSRF BL19U1
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 2.5 50 99.9 0.043 0.997 32.22 6.4 13097
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 2.5 2.59 98 0.851 0.897 1.86 5.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7YHL 2.5 28.91 13090 683 98.785 0.259 0.2578 0.2565 0.2786 0.2717 RANDOM 114.148
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] -3.444 0.787 7.902 -4.259
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.288 r_lrange_other 30.287 r_scangle_it 25.293 r_scangle_other 25.287 r_mcangle_it 24.183 r_mcangle_other 24.177 r_mcbond_it 18.545 r_mcbond_other 18.544 r_scbond_it 18.532 r_scbond_other 18.53
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.288 r_lrange_other 30.287 r_scangle_it 25.293 r_scangle_other 25.287 r_mcangle_it 24.183 r_mcangle_other 24.177 r_mcbond_it 18.545 r_mcbond_other 18.544 r_scbond_it 18.532 r_scbond_other 18.53 r_dihedral_angle_6_deg 16.47 r_dihedral_angle_3_deg 15.693 r_dihedral_angle_1_deg 8.437 r_dihedral_angle_2_deg 5.953 r_angle_refined_deg 1.759 r_angle_other_deg 0.626 r_symmetry_xyhbond_nbd_refined 0.259 r_nbd_other 0.234 r_symmetry_nbd_other 0.207 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.175 r_nbd_refined 0.155 r_symmetry_nbd_refined 0.103 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.013 r_bond_refined_d 0.01 r_bond_other_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2856 Nucleic Acid Atoms 88 Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing Coot model building PHENIX model building HKL-2000 data reduction