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Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with cyclic-tetraadenylate (cA4)
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, 22% w/v Polyethylene glycol monomethyl ether 550, 5% w/v n-Dodecyl-B-D-maltoside
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.052 α = 90 b = 38.837 β = 105.798 c = 72.965 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 2022-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 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 3.11 50 99.57 0.07 0.997 22.84 3.7 6715
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 3.11 3.22 100 0.786 0.602 1.88
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 3.11 28.556 6710 328 99.54 0.239 0.2379 0.2368 0.2584 0.2547 RANDOM 136.267
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] -1.611 3.216 -0.998 0.681
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 38.41 r_lrange_other 38.409 r_mcangle_it 30.398 r_mcangle_other 30.391 r_scangle_it 29.122 r_scangle_other 29.116 r_mcbond_it 21.768 r_mcbond_other 21.768 r_scbond_it 19.825 r_scbond_other 19.821
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 38.41 r_lrange_other 38.409 r_mcangle_it 30.398 r_mcangle_other 30.391 r_scangle_it 29.122 r_scangle_other 29.116 r_mcbond_it 21.768 r_mcbond_other 21.768 r_scbond_it 19.825 r_scbond_other 19.821 r_dihedral_angle_6_deg 16.526 r_dihedral_angle_3_deg 16.191 r_dihedral_angle_1_deg 9.048 r_dihedral_angle_2_deg 5.948 r_angle_refined_deg 1.71 r_angle_other_deg 0.65 r_symmetry_xyhbond_nbd_refined 0.284 r_nbd_other 0.231 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.175 r_nbd_refined 0.169 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.021 r_bond_refined_d 0.01 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2850 Nucleic Acid Atoms 88 Solvent Atoms 1 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