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Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E PDB entry 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 30% PEG2000 MME, 0.1 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.81 α = 90 b = 53.54 β = 98.92 c = 45.33 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 PILATUS3 S 6M 2021-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.52131 CLSI 08B1-1
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 2.6 38.4 93.18 0.996 6 1.9 8666
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 2.6 2.693 48.82 0.679 0.45 1.9
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 (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 PDB entry 6Y2E 2.6 38.4 8103 443 98.63 0.22339 0.22036 0.2226 0.27853 0.2757 RANDOM 60.609
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] 3.43 -1.21 -1.7 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.856 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 6.73 r_long_range_B_refined 5.479 r_long_range_B_other 5.475 r_mcangle_it 3.07 r_mcangle_other 3.07 r_scangle_other 2.797 r_mcbond_it 1.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.856 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 6.73 r_long_range_B_refined 5.479 r_long_range_B_other 5.475 r_mcangle_it 3.07 r_mcangle_other 3.07 r_scangle_other 2.797 r_mcbond_it 1.752 r_mcbond_other 1.749 r_scbond_it 1.562 r_scbond_other 1.561 r_angle_refined_deg 1.22 r_angle_other_deg 1.059 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2347 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing