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Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.4 M Sodium acetate trihydrate, pH 5.8, 30% PEG 400, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 1.99 38.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.673 α = 90 b = 53.09 β = 101.96 c = 45.774 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 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (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 2.067 55.6 99.5 0.108 5.98 6.9 16462
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 2.067 2.1 0.28 0.26
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 2.067 55.6 15835 626 99.74 0.19413 0.19191 0.1817 0.24028 0.2479 RANDOM 59.194
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] 1.57 0.23 0.49 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.483 r_dihedral_angle_2_deg 12.894 r_long_range_B_refined 10.394 r_long_range_B_other 10.392 r_dihedral_angle_1_deg 8.16 r_scangle_other 7.583 r_mcangle_it 6.229 r_mcangle_other 6.227 r_scbond_it 4.869 r_scbond_other 4.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.483 r_dihedral_angle_2_deg 12.894 r_long_range_B_refined 10.394 r_long_range_B_other 10.392 r_dihedral_angle_1_deg 8.16 r_scangle_other 7.583 r_mcangle_it 6.229 r_mcangle_other 6.227 r_scbond_it 4.869 r_scbond_other 4.867 r_mcbond_it 4.205 r_mcbond_other 4.204 r_angle_refined_deg 1.47 r_angle_other_deg 0.586 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2365 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing