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Crystal Structure of Nsp15 Endoribonuclease from SARS CoV-2 in Complex with TAS-103
X-RAY DIFFRACTION - SOLUTION SCATTERING
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.1 mM sodium phosphate pH 6.5
10 % w/v Peg 8000
0.3 M NaCl
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.488 α = 90 b = 150.488 β = 90 c = 110.086 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 EIGER2 X 16M 2022-06-13 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) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 49.26 99.9 0.098 0.989 7.7 4.7 95339
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 0.868 0.625
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2 49.26 90542 4755 99.76 0.16239 0.16162 0.1691 0.17693 0.182 RANDOM 48.021
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] -7.33 -7.33 14.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.057 r_dihedral_angle_2_deg 7.194 r_dihedral_angle_1_deg 6.555 r_long_range_B_other 6.32 r_long_range_B_refined 6.318 r_scangle_other 4.729 r_scbond_other 3.212 r_scbond_it 3.211 r_mcangle_it 3.025 r_mcangle_other 3.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.057 r_dihedral_angle_2_deg 7.194 r_dihedral_angle_1_deg 6.555 r_long_range_B_other 6.32 r_long_range_B_refined 6.318 r_scangle_other 4.729 r_scbond_other 3.212 r_scbond_it 3.211 r_mcangle_it 3.025 r_mcangle_other 3.025 r_mcbond_it 2.206 r_mcbond_other 2.205 r_angle_refined_deg 1.167 r_angle_other_deg 0.418 r_chiral_restr 0.059 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 5475 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction