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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WTT
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 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.117 α = 90 b = 87.231 β = 104.49 c = 107.558 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 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 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 2.23 50 97.9 0.147 10.22 3.9 60743
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 2.23 2.27 94.6 0.518 2.13 3.4
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 2.23 47.71 57640 3081 97.52 0.18228 0.17965 0.187 0.23138 0.238 RANDOM 30.323
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] 1.96 -0.98 -2.48 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.882 r_dihedral_angle_1_deg 7.324 r_long_range_B_refined 7.034 r_long_range_B_other 7.03 r_dihedral_angle_2_deg 6.215 r_scangle_other 5 r_mcangle_it 3.979 r_mcangle_other 3.979 r_scbond_it 3.039 r_scbond_other 3.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.882 r_dihedral_angle_1_deg 7.324 r_long_range_B_refined 7.034 r_long_range_B_other 7.03 r_dihedral_angle_2_deg 6.215 r_scangle_other 5 r_mcangle_it 3.979 r_mcangle_other 3.979 r_scbond_it 3.039 r_scbond_other 3.039 r_mcbond_it 2.469 r_mcbond_other 2.468 r_angle_refined_deg 1.293 r_angle_other_deg 0.437 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9480 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing