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Crystal structure of the SARS-CoV-2 Main Protease with a Zinc ion coordinated in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.31 α = 90 b = 53.68 β = 101.67 c = 44.72 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 2020-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978564 SOLEIL PROXIMA 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 1.815 48.37 99 0.998 12.8 6.9 23721
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 1.815 1.85 94.2 0.423
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K3T 1.815 48.37 23721 1186 99.114 0.2 0.1966 0.1969 0.257 0.2586 38.006
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] 1.697 0.097 0.197 -1.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.47 r_dihedral_angle_4_deg 14.837 r_dihedral_angle_3_deg 13.21 r_dihedral_angle_1_deg 7.882 r_lrange_it 6.784 r_lrange_other 6.729 r_scangle_it 4.779 r_scangle_other 4.779 r_mcangle_it 3.841 r_mcangle_other 3.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.47 r_dihedral_angle_4_deg 14.837 r_dihedral_angle_3_deg 13.21 r_dihedral_angle_1_deg 7.882 r_lrange_it 6.784 r_lrange_other 6.729 r_scangle_it 4.779 r_scangle_other 4.779 r_mcangle_it 3.841 r_mcangle_other 3.84 r_scbond_it 3.274 r_scbond_other 3.268 r_mcbond_it 2.836 r_mcbond_other 2.835 r_angle_refined_deg 1.461 r_angle_other_deg 1.305 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.2 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2351 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing XDS data processing Coot model building