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Crystal structure of the SARS-CoV-2 Main Protease with oxidized C145
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 1.95 36.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.69 α = 90 b = 52.96 β = 102.95 c = 44.85 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 1.477 47.828 97.1 0.998 11.7 7.1 42473
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 1.48 1.57 93.6 0.7
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 1.477 47.828 42468 2124 97.207 0.168 0.1657 0.164 0.2072 0.2073 21.072
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] 0.82 -0.64 0.061 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 12.733 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 7.483 r_angle_refined_deg 1.7 r_angle_other_deg 1.516 r_nbd_refined 0.217 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.277 r_dihedral_angle_4_deg 12.733 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 7.483 r_angle_refined_deg 1.7 r_angle_other_deg 1.516 r_nbd_refined 0.217 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.156 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing XDS data processing Coot model building