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Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in complex with its post-catalytic reaction product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2M KSCN
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.731 α = 90 b = 56.731 β = 90 c = 361.469 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 16M 2020-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 61.52 93.5 0.99 9.3 7.8 14426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.92 0.37
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 FREE R-VALUE 7PQ2 2.85 48.05 14031 740 99.187 0.254 0.2515 0.2497 0.2906 0.2869 117.141
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] -0.595 -0.595 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_3_deg 21.725 r_dihedral_angle_4_deg 18.63 r_lrange_it 11.251 r_lrange_other 11.25 r_dihedral_angle_1_deg 6.863 r_scangle_it 5.195 r_scangle_other 5.194 r_mcangle_it 4.716 r_mcangle_other 4.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_3_deg 21.725 r_dihedral_angle_4_deg 18.63 r_lrange_it 11.251 r_lrange_other 11.25 r_dihedral_angle_1_deg 6.863 r_scangle_it 5.195 r_scangle_other 5.194 r_mcangle_it 4.716 r_mcangle_other 4.716 r_scbond_it 3.098 r_scbond_other 3.098 r_mcbond_it 2.763 r_mcbond_other 2.763 r_angle_refined_deg 1.638 r_angle_other_deg 1.284 r_nbd_other 0.233 r_symmetry_nbd_refined 0.225 r_symmetry_nbd_other 0.214 r_nbd_refined 0.205 r_nbtor_refined 0.174 r_ncsr_local_group_1 0.159 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_refined 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4358 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing