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Crystal structure of SARS-CoV-2 main protease T21I/E166V 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 Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.34 α = 90 b = 105.787 β = 102.922 c = 54.208 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 1.95 47.27 90.5 0.093 0.998 14.5 6.2 35017
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 1.95 2 0.701 0.6 2.7
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 1.95 47.16 34951 1780 90.373 0.178 0.175 0.1815 0.2286 0.2325 31.044
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] -0.082 0.869 -0.748 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.883 r_dihedral_angle_6_deg 14.165 r_dihedral_angle_3_deg 13.897 r_lrange_other 8.733 r_lrange_it 8.727 r_dihedral_angle_1_deg 7.349 r_scangle_it 6.045 r_scangle_other 6.045 r_mcangle_other 4.721 r_mcangle_it 4.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.883 r_dihedral_angle_6_deg 14.165 r_dihedral_angle_3_deg 13.897 r_lrange_other 8.733 r_lrange_it 8.727 r_dihedral_angle_1_deg 7.349 r_scangle_it 6.045 r_scangle_other 6.045 r_mcangle_other 4.721 r_mcangle_it 4.72 r_scbond_it 4.034 r_scbond_other 4.034 r_mcbond_it 3.293 r_mcbond_other 3.291 r_dihedral_angle_other_3_deg 2.019 r_angle_refined_deg 1.674 r_angle_other_deg 0.595 r_symmetry_nbd_refined 0.3 r_nbd_other 0.223 r_nbd_refined 0.22 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_1 0.088 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.057 r_gen_planes_refined 0.009 r_bond_refined_d 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 4708 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing