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Crystal structure of SARS-CoV-2 main protease 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, SITTING DROP 289 20% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 2% v/v Polyethylene glycol 200. Protein concentration 8 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.17 α = 90 b = 105.998 β = 103.031 c = 54.449 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 1.65 106 98.3 0.068 0.994 10.5 6.1 62740
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 1.65 1.68 0.71 0.786 2.1
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 1.65 53.047 62647 3076 98.104 0.195 0.1931 0.2016 0.2384 0.2397 23.032
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] -0.471 1.027 -0.2 0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.833 r_dihedral_angle_6_deg 14.378 r_dihedral_angle_3_deg 11.675 r_dihedral_angle_1_deg 7.394 r_lrange_it 5.68 r_lrange_other 5.628 r_scangle_it 4.145 r_scangle_other 4.145 r_dihedral_angle_other_3_deg 3.42 r_mcangle_it 3.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.833 r_dihedral_angle_6_deg 14.378 r_dihedral_angle_3_deg 11.675 r_dihedral_angle_1_deg 7.394 r_lrange_it 5.68 r_lrange_other 5.628 r_scangle_it 4.145 r_scangle_other 4.145 r_dihedral_angle_other_3_deg 3.42 r_mcangle_it 3.028 r_mcangle_other 3.028 r_scbond_it 2.778 r_scbond_other 2.777 r_mcbond_it 2.058 r_mcbond_other 2.056 r_angle_refined_deg 1.744 r_angle_other_deg 0.59 r_nbd_refined 0.214 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.186 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_refined 0.083 r_symmetry_xyhbond_nbd_other 0.064 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 4707 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing