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Crystal structure of SARS-CoV-2 main protease M49I/M165T mutant in complex with leritrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M Magnesium chloride hexahydrate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.06 40.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.427 α = 90 b = 106.197 β = 103.173 c = 54.289 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 2024-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 53.1 91.3 0.105 0.998 16.7 6.5 32890
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 1.26 0.772 2.3
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 2 53.098 32727 1642 90.724 0.167 0.1642 0.1738 0.2197 0.2232 26.068
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] -0.577 1.244 -0.753 0.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.987 r_dihedral_angle_6_deg 13.766 r_dihedral_angle_3_deg 12.363 r_lrange_it 7.257 r_dihedral_angle_1_deg 7.232 r_lrange_other 7.226 r_scangle_it 5.081 r_scangle_other 5.08 r_mcangle_it 3.502 r_mcangle_other 3.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.987 r_dihedral_angle_6_deg 13.766 r_dihedral_angle_3_deg 12.363 r_lrange_it 7.257 r_dihedral_angle_1_deg 7.232 r_lrange_other 7.226 r_scangle_it 5.081 r_scangle_other 5.08 r_mcangle_it 3.502 r_mcangle_other 3.501 r_scbond_it 3.322 r_scbond_other 3.322 r_mcbond_it 2.405 r_mcbond_other 2.404 r_dihedral_angle_other_3_deg 1.676 r_angle_refined_deg 1.52 r_angle_other_deg 0.533 r_symmetry_nbd_refined 0.296 r_nbd_other 0.236 r_nbd_refined 0.209 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 r_ncsr_local_group_1 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 4711 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing