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Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7 PDB entry 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 0.1 M MES, pH 6.0, 20.0% w/v PEG6000, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.61 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.83 α = 90 b = 100.61 β = 90 c = 103.42 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 PIXEL DECTRIS EIGER X 9M 2020-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 1.626 72.115 65.8 0.998 12.5 6.6 59000
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 1.626 1.732 0.564
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 6LU7 1.626 72.11 59000 3022 65.9 0.1955 0.1937 0.1964 0.2281 0.2298 RANDOM 25.71
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] 0.0198 -0.3804 0.3606
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.25 t_omega_torsion 3.87 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4696 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 86
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling BUSTER phasing