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Crystal structure of SARS-CoV-2 main protease L50F/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 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.464 α = 90 b = 106.553 β = 103.015 c = 54.133 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 2.5 53.28 98.8 0.148 0.995 10.9 6 18373
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 2.5 2.6 0.932 0.39 1.7
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 2.5 53.277 18321 905 98.601 0.181 0.1776 0.1843 0.2463 0.2446 49.572
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] 0.332 1.573 -1.296 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.635 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_6_deg 13.903 r_lrange_other 10.83 r_lrange_it 10.828 r_dihedral_angle_1_deg 7.685 r_mcangle_it 6.594 r_mcangle_other 6.594 r_scangle_it 6.252 r_scangle_other 6.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.635 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_6_deg 13.903 r_lrange_other 10.83 r_lrange_it 10.828 r_dihedral_angle_1_deg 7.685 r_mcangle_it 6.594 r_mcangle_other 6.594 r_scangle_it 6.252 r_scangle_other 6.251 r_mcbond_it 4.148 r_mcbond_other 4.143 r_scbond_it 3.982 r_scbond_other 3.981 r_angle_refined_deg 1.397 r_angle_other_deg 0.481 r_nbd_refined 0.215 r_symmetry_nbd_other 0.201 r_nbd_other 0.185 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.165 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.118 r_dihedral_angle_other_3_deg 0.106 r_ncsr_local_group_1 0.105 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.005 r_gen_planes_refined 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 4630 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing