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Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG3000, 0.1M CHES pH 9.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.372 α = 90 b = 106.436 β = 102.919 c = 78.443 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 2019-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.98 MAX IV BioMAX
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 2.38 61.73 99.9 0.99 14.1 7 24724
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 2.38 2.43 0.756
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 3QYF 2.38 61.61 23654 1176 95.084 0.166 0.1634 0.1634 0.2226 0.2226 42.532
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] 0.032 0.004 -0.033 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.116 r_dihedral_angle_4_deg 21.626 r_dihedral_angle_3_deg 18.298 r_lrange_it 8.973 r_dihedral_angle_1_deg 6.239 r_scangle_it 5.916 r_mcangle_it 4.043 r_scbond_it 3.76 r_mcbond_it 2.544 r_angle_refined_deg 1.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.116 r_dihedral_angle_4_deg 21.626 r_dihedral_angle_3_deg 18.298 r_lrange_it 8.973 r_dihedral_angle_1_deg 6.239 r_scangle_it 5.916 r_mcangle_it 4.043 r_scbond_it 3.76 r_mcbond_it 2.544 r_angle_refined_deg 1.776 r_nbtor_refined 0.32 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.193 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.151 r_ncsr_local_group_1 0.14 r_chiral_restr 0.124 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4442 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing