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Crystal structure of SARS-CoV-2 main protease M49T 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 0.1 M Tris pH 8.0, 30% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.784 α = 90 b = 106.314 β = 103.002 c = 54.055 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 1.7 52.725 94 0.113 0.991 8.6 4.2 55394
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 1.7 1.73 0.557 0.635 2
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 1.7 52.725 55340 2751 93.92 0.173 0.1705 0.1785 0.2165 0.2208 20.87
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] -0.076 0.918 -0.088 -0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.255 r_dihedral_angle_6_deg 13.239 r_dihedral_angle_3_deg 12.716 r_dihedral_angle_1_deg 6.954 r_lrange_it 6.371 r_lrange_other 6.114 r_scangle_it 4.078 r_scangle_other 4.078 r_mcangle_it 3.126 r_mcangle_other 3.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.255 r_dihedral_angle_6_deg 13.239 r_dihedral_angle_3_deg 12.716 r_dihedral_angle_1_deg 6.954 r_lrange_it 6.371 r_lrange_other 6.114 r_scangle_it 4.078 r_scangle_other 4.078 r_mcangle_it 3.126 r_mcangle_other 3.126 r_scbond_it 2.605 r_scbond_other 2.605 r_mcbond_it 2.042 r_mcbond_other 2.04 r_angle_refined_deg 1.594 r_dihedral_angle_other_3_deg 1.269 r_angle_other_deg 0.535 r_symmetry_nbd_refined 0.221 r_nbd_refined 0.213 r_nbd_other 0.199 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.166 r_ncsr_local_group_1 0.092 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4783 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing