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Crystal structure of SARS-CoV-2 main protease 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 0.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2 38.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.003 α = 90 b = 53.078 β = 102.17 c = 45.783 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 2022-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
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 1.74 55.72 99.85 0.9989 11.9 8.6 27421
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 1.74 1.77 0.3184
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 1.74 55.72 26028 1393 99.82 0.19602 0.1939 0.2015 0.23299 0.2398 RANDOM 46.261
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] 1.46 -0.17 0.24 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.856 r_dihedral_angle_2_deg 12.048 r_long_range_B_refined 10.809 r_long_range_B_other 10.807 r_scangle_other 8.989 r_dihedral_angle_1_deg 7.773 r_scbond_it 6.456 r_scbond_other 6.454 r_mcangle_it 6.214 r_mcangle_other 6.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.856 r_dihedral_angle_2_deg 12.048 r_long_range_B_refined 10.809 r_long_range_B_other 10.807 r_scangle_other 8.989 r_dihedral_angle_1_deg 7.773 r_scbond_it 6.456 r_scbond_other 6.454 r_mcangle_it 6.214 r_mcangle_other 6.212 r_mcbond_it 4.936 r_mcbond_other 4.934 r_angle_refined_deg 2.144 r_angle_other_deg 0.792 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 2367 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction CrystalClear data scaling MOLREP phasing