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Crystal Structure of SARS-CoV-2 Main protease A193S mutant in complex with Nirmatrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M MES pH 6.7, 5% DMSO, 8% PEG 4000 Cryo protected with 40% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.63 53.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.905 α = 90 b = 103.925 β = 90 c = 68.025 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 2M 2022-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRUS BEAMLINE MANACA 0.977180 LNLS SIRUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.48 72.5 59.5 0.965 3.9 6.4 15497
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.57 0.575
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7mbg 2.48 72.5 15481 765 59.506 0.219 0.2166 0.2166 0.2723 0.2725 31.165
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] 0.386 -0.336 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.677 r_dihedral_angle_4_deg 19.976 r_dihedral_angle_3_deg 17.156 r_dihedral_angle_1_deg 7.569 r_lrange_it 5.647 r_lrange_other 5.647 r_mcangle_it 3.175 r_mcangle_other 3.174 r_scangle_it 2.896 r_scangle_other 2.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.677 r_dihedral_angle_4_deg 19.976 r_dihedral_angle_3_deg 17.156 r_dihedral_angle_1_deg 7.569 r_lrange_it 5.647 r_lrange_other 5.647 r_mcangle_it 3.175 r_mcangle_other 3.174 r_scangle_it 2.896 r_scangle_other 2.896 r_mcbond_it 1.781 r_mcbond_other 1.781 r_scbond_it 1.638 r_scbond_other 1.637 r_angle_refined_deg 1.487 r_angle_other_deg 1.301 r_nbd_other 0.538 r_symmetry_nbd_refined 0.504 r_symmetry_xyhbond_nbd_other 0.414 r_symmetry_nbd_other 0.208 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4669 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing