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Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Narlaprevir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 22% PEG 4000, 100 mM HEPES pH 7.0, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 1.96 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.188 α = 90 b = 52.507 β = 102.71 c = 45.693 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 2020-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.79 27.62 98 0.079 0.092 0.047 0.998 10.5 3.7 24134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 79.8 1.199 1.411 0.732 0.545 3.3
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 6XQS 1.79 27.6 22844 1224 97.59 0.1769 0.175 0.1883 0.2125 0.2211 RANDOM 31.109
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] -0.01 -0.03 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.581 r_dihedral_angle_4_deg 20.307 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_1_deg 7.559 r_angle_refined_deg 1.625 r_angle_other_deg 1.39 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.581 r_dihedral_angle_4_deg 20.307 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_1_deg 7.559 r_angle_refined_deg 1.625 r_angle_other_deg 1.39 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction