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Crystal structure of the SARS-CoV-2 (COVID-19) main protease (Mpro) in complex with inhibitor Jun89-3-C1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 2.01 38.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.365 α = 90 b = 53.725 β = 101.38 c = 113.799 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 PILATUS3 6M 2022-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.08 50 98.3 0.074 21.39 3.9 32051
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 99.2 0.493 2.2 3.8
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 (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 2.08 48.45 30435 1606 98.19 0.20606 0.20325 0.2182 0.25867 0.2686 RANDOM 49.946
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] 2.38 1.24 -3.36 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.95 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_3_deg 15.437 r_long_range_B_refined 7.231 r_long_range_B_other 7.224 r_dihedral_angle_1_deg 6.966 r_scangle_other 4.947 r_scbond_it 3.615 r_scbond_other 3.615 r_mcangle_it 3.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.95 r_dihedral_angle_4_deg 19.714 r_dihedral_angle_3_deg 15.437 r_long_range_B_refined 7.231 r_long_range_B_other 7.224 r_dihedral_angle_1_deg 6.966 r_scangle_other 4.947 r_scbond_it 3.615 r_scbond_other 3.615 r_mcangle_it 3.558 r_mcangle_other 3.558 r_mcbond_it 2.504 r_mcbond_other 2.5 r_angle_refined_deg 1.521 r_angle_other_deg 1.134 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 4696 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing