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Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 22% PEG 4000
0.05 M Tricine pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.83 32.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.423 α = 90 b = 51 β = 98.696 c = 80.353 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 EIGER X 16M 2020-06-23 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 1.91 79.43 85.2 0.995 9.7 6.3 19381
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 1.91 2.05 0.191
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 7Z55 2.27 79.429 15733 776 98.801 0.185 0.1815 0.1849 0.2534 0.2528 54.421
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] 0.316 -0.287 -0.496 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.738 r_dihedral_angle_4_deg 22.807 r_dihedral_angle_3_deg 20.646 r_lrange_it 8.955 r_lrange_other 8.953 r_dihedral_angle_1_deg 7.328 r_scangle_it 6.796 r_scangle_other 6.794 r_mcangle_it 4.63 r_mcangle_other 4.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.738 r_dihedral_angle_4_deg 22.807 r_dihedral_angle_3_deg 20.646 r_lrange_it 8.955 r_lrange_other 8.953 r_dihedral_angle_1_deg 7.328 r_scangle_it 6.796 r_scangle_other 6.794 r_mcangle_it 4.63 r_mcangle_other 4.629 r_scbond_it 4.11 r_scbond_other 4.109 r_mcbond_it 3.157 r_mcbond_other 3.146 r_angle_refined_deg 1.829 r_angle_other_deg 1.373 r_nbd_refined 0.218 r_nbd_other 0.202 r_symmetry_nbd_other 0.196 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_refined 0.178 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.167 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2851 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing