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Structure of the SARS-CoV-2 main protease in complex with AG7404
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Sodium chloride, HEPES pH 7 and PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.309 α = 90 b = 54.082 β = 100.34 c = 115.011 γ = 90
Symmetry Space Group P 1 21 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 4M 2021-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 2.26 48.84 89.5 0.985 4.5 2.5 18801
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 2.26 2.45 0.802
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 6y2e 2.26 48.84 17928 873 72.67 0.19252 0.1902 0.1957 0.24054 0.2443 RANDOM 40.67
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] 0.09 -0.11 -0.39 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.101 r_dihedral_angle_4_deg 19.643 r_dihedral_angle_3_deg 17.954 r_dihedral_angle_1_deg 7.98 r_long_range_B_refined 7.791 r_long_range_B_other 7.79 r_scangle_other 5.186 r_mcangle_it 4.505 r_mcangle_other 4.505 r_scbond_it 3.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.101 r_dihedral_angle_4_deg 19.643 r_dihedral_angle_3_deg 17.954 r_dihedral_angle_1_deg 7.98 r_long_range_B_refined 7.791 r_long_range_B_other 7.79 r_scangle_other 5.186 r_mcangle_it 4.505 r_mcangle_other 4.505 r_scbond_it 3.214 r_scbond_other 3.214 r_mcbond_it 2.815 r_mcbond_other 2.814 r_angle_refined_deg 1.444 r_angle_other_deg 1.194 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing