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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F 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 1.98 37.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.228 α = 90 b = 105.474 β = 104.5 c = 53.792 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 2022-09-22 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 2.21 50 99.4 0.133 17.3 6.2 25847
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 2.22 2.26 0.517 2.41 4.4
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 2.21 46.74 24493 1332 98.64 0.18191 0.17884 0.1855 0.23876 0.2443 RANDOM 46.782
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] 0.94 3.88 -3.15 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.585 r_long_range_B_refined 8.622 r_long_range_B_other 8.622 r_dihedral_angle_1_deg 7.504 r_scangle_other 6.435 r_dihedral_angle_2_deg 5.294 r_mcangle_it 5.201 r_mcangle_other 5.201 r_scbond_it 4.086 r_scbond_other 4.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.585 r_long_range_B_refined 8.622 r_long_range_B_other 8.622 r_dihedral_angle_1_deg 7.504 r_scangle_other 6.435 r_dihedral_angle_2_deg 5.294 r_mcangle_it 5.201 r_mcangle_other 5.201 r_scbond_it 4.086 r_scbond_other 4.086 r_mcbond_it 3.494 r_mcbond_other 3.493 r_angle_refined_deg 1.418 r_angle_other_deg 0.473 r_chiral_restr 0.064 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 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 4742 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing