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Crystal structure of SARS-CoV-2 main protease P168 deletion and A173V 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, HANGING DROP 289 0.1M Sodium acetate trihydrate pH 8.0, 16% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.751 α = 90 b = 53.166 β = 102.715 c = 46.271 γ = 90
Symmetry Space Group C 1 2 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 2024-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97907 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 2.2 48.07 99.1 0.1439 0.9918 15.45 6.48 14491
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 2.27 0.4743 0.8382 4.54
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 2.2 48.07 13816 663 99.054 0.173 0.1701 0.1781 0.2383 0.2459 31.479
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] 0.75 -1.097 -0.929 0.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.443 r_dihedral_angle_6_deg 14.701 r_dihedral_angle_3_deg 13.676 r_dihedral_angle_1_deg 8.518 r_lrange_it 8.126 r_lrange_other 8.124 r_scangle_it 5.537 r_scangle_other 5.535 r_mcangle_it 4.312 r_mcangle_other 4.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.443 r_dihedral_angle_6_deg 14.701 r_dihedral_angle_3_deg 13.676 r_dihedral_angle_1_deg 8.518 r_lrange_it 8.126 r_lrange_other 8.124 r_scangle_it 5.537 r_scangle_other 5.535 r_mcangle_it 4.312 r_mcangle_other 4.312 r_scbond_it 3.611 r_scbond_other 3.61 r_mcbond_it 2.939 r_mcbond_other 2.932 r_dihedral_angle_other_3_deg 2.147 r_angle_refined_deg 1.78 r_angle_other_deg 0.603 r_nbd_refined 0.231 r_nbd_other 0.22 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.099 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.088 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 2295 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing