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Crystal Structure of nsp15 Endoribonuclease from SARS CoV-2 in Complex with Sepantronium (YM-155)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.1 M Tris pH 8.5, 10 % w/v Peg 4000, 0.15 mM sodium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.408 α = 90 b = 151.408 β = 90 c = 109.302 γ = 120
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 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.08 45.14 99.7 0.064 0.077 0.999 12.6 5.8 85181
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 99.9 1.396 0.936 0.502
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) 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 2.08 45.14 80915 4240 99.7 0.19198 0.19133 0.1972 0.20526 0.21 RANDOM 53.512
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] -11.52 -11.52 23.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.982 r_dihedral_angle_1_deg 6.107 r_long_range_B_refined 3.374 r_long_range_B_other 3.374 r_dihedral_angle_2_deg 1.829 r_mcangle_it 1.32 r_mcangle_other 1.319 r_scangle_other 1.249 r_mcbond_it 0.764 r_mcbond_other 0.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.982 r_dihedral_angle_1_deg 6.107 r_long_range_B_refined 3.374 r_long_range_B_other 3.374 r_dihedral_angle_2_deg 1.829 r_mcangle_it 1.32 r_mcangle_other 1.319 r_scangle_other 1.249 r_mcbond_it 0.764 r_mcbond_other 0.764 r_scbond_it 0.714 r_scbond_other 0.714 r_angle_refined_deg 0.708 r_angle_other_deg 0.287 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4833 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing