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Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C63
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 6.5 295 0.1 M BTP, pH 6.5, 20% PEG3350, 0.2 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.01 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.45 α = 90 b = 53.318 β = 101.88 c = 45.474 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 EIGER2 X 16M 2021-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 2.5 48.11 97.9 0.998 12.52 2.8 9329
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 2.5 2.59 99.1 0.786 1.3
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 2.5 48.11 8670 434 97.6 0.22899 0.224 0.2276 0.268 0.2646 RANDOM 59.42
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] -0.98 -1.6 0.82 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.914 r_dihedral_angle_4_deg 18.516 r_dihedral_angle_3_deg 13.995 r_dihedral_angle_1_deg 7.02 r_scangle_other 5.406 r_mcangle_it 5.396 r_mcangle_other 5.395 r_mcbond_it 3.173 r_mcbond_other 3.173 r_scbond_it 3.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.914 r_dihedral_angle_4_deg 18.516 r_dihedral_angle_3_deg 13.995 r_dihedral_angle_1_deg 7.02 r_scangle_other 5.406 r_mcangle_it 5.396 r_mcangle_other 5.395 r_mcbond_it 3.173 r_mcbond_other 3.173 r_scbond_it 3.154 r_scbond_other 3.153 r_angle_other_deg 1.239 r_angle_refined_deg 1.237 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 28 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing