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Crystal Structure of the Ring Nuclease 0811 mutant-S12A from Sulfolobus islandicus (Sis0811)
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 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.054 α = 90 b = 103.735 β = 102.99 c = 77.678 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2020-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 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 2.67 60.82 98 0.945 6.7 6.3 16673
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 2.67 2.714 0.494
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 2.67 60.82 16225 839 95.531 0.223 0.22 0.2195 0.2795 0.2744 38.112
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] -0.23 -0.068 -0.094 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.938 r_dihedral_angle_4_deg 24.812 r_dihedral_angle_3_deg 18.366 r_dihedral_angle_1_deg 7.436 r_lrange_it 5.784 r_lrange_other 5.784 r_mcangle_it 3.413 r_mcangle_other 3.413 r_scangle_it 2.996 r_scangle_other 2.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.938 r_dihedral_angle_4_deg 24.812 r_dihedral_angle_3_deg 18.366 r_dihedral_angle_1_deg 7.436 r_lrange_it 5.784 r_lrange_other 5.784 r_mcangle_it 3.413 r_mcangle_other 3.413 r_scangle_it 2.996 r_scangle_other 2.996 r_mcbond_it 1.954 r_mcbond_other 1.952 r_scbond_it 1.726 r_scbond_other 1.725 r_angle_refined_deg 1.602 r_angle_other_deg 1.256 r_nbd_other 0.283 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.205 r_symmetry_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.17 r_ncsr_local_group_1 0.155 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.101 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4440 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing