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Crystal structure of the SARS-CoV-2 Main Protease inhibited by (2-methylsulfanyl-6,7-dihydro-[1,4]dioxino[2,3-f]benzimidazol-3-yl)-(p-tolyl)methanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG3350, 0.2 M Sodium Formate, 2.5 mM DMSO
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.247 α = 90 b = 54.004 β = 101.142 c = 44.68 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 9M 2021-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 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 1.7 43.84 99.8 0.095 0.12 0.072 0.993 8.4 5.1 29703
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.9 0.89 0.667 0.631 1.3 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 38.455 29702 1515 99.738 0.191 0.1892 0.1858 0.2344 0.2304 18.189
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] 0.386 -0.701 0.285 -0.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.631 r_dihedral_angle_6_deg 15.309 r_dihedral_angle_3_deg 12.873 r_lrange_it 7.146 r_lrange_other 7.091 r_dihedral_angle_1_deg 7.066 r_scangle_it 5.303 r_scangle_other 5.302 r_scbond_other 3.604 r_scbond_it 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.631 r_dihedral_angle_6_deg 15.309 r_dihedral_angle_3_deg 12.873 r_lrange_it 7.146 r_lrange_other 7.091 r_dihedral_angle_1_deg 7.066 r_scangle_it 5.303 r_scangle_other 5.302 r_scbond_other 3.604 r_scbond_it 3.6 r_mcangle_it 3.069 r_mcangle_other 3.068 r_angle_refined_deg 2.418 r_mcbond_it 2.116 r_mcbond_other 2.115 r_angle_other_deg 0.836 r_dihedral_angle_other_3_deg 0.36 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_refined 0.23 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.167 r_nbd_other 0.161 r_symmetry_nbd_refined 0.143 r_chiral_restr 0.12 r_symmetry_nbtor_other 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2302 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction MxCuBE data collection