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Crystal structure of SARS-CoV-2 main protease M49I/M165I 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 Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.394 α = 90 b = 106.198 β = 102.815 c = 54.431 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 1.8 53.1 99.4 0.141 0.997 11.1 6.4 49316
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 1.8 1.84 0.9 0.469 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 1.8 53.099 49254 2436 99.324 0.178 0.176 0.1835 0.2186 0.2224 19.37
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] 0.153 0.603 -0.121 -0.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.654 r_dihedral_angle_6_deg 14.567 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 7.251 r_lrange_it 6.459 r_lrange_other 6.386 r_scangle_it 4.061 r_scangle_other 4.06 r_mcangle_other 2.71 r_mcangle_it 2.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.654 r_dihedral_angle_6_deg 14.567 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 7.251 r_lrange_it 6.459 r_lrange_other 6.386 r_scangle_it 4.061 r_scangle_other 4.06 r_mcangle_other 2.71 r_mcangle_it 2.707 r_scbond_it 2.54 r_scbond_other 2.539 r_mcbond_it 1.718 r_mcbond_other 1.71 r_angle_refined_deg 1.54 r_dihedral_angle_other_3_deg 1.188 r_angle_other_deg 0.528 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.181 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.164 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_other 0.105 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.083 r_chiral_restr 0.076 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4719 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing