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Crystal Structure of SARS-CoV-2 Main protease mutant Q189K 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% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400
Crystal Properties Matthews coefficient Solvent content 2.63 53.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.782 α = 90 b = 101.572 β = 90 c = 103.561 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 2.366 72.52 56.9 0.997 4.6 5.3 16996
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 2.366 2.45 0.683
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 2.366 72.515 16996 1700 56.906 0.235 0.2286 0.2285 0.2961 0.296 31.972
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] -0.194 0.236 -0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_4_deg 25.075 r_dihedral_angle_3_deg 16.796 r_dihedral_angle_1_deg 7.801 r_lrange_other 4.714 r_lrange_it 4.698 r_scangle_it 2.715 r_scangle_other 2.714 r_mcangle_it 2.701 r_mcangle_other 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_4_deg 25.075 r_dihedral_angle_3_deg 16.796 r_dihedral_angle_1_deg 7.801 r_lrange_other 4.714 r_lrange_it 4.698 r_scangle_it 2.715 r_scangle_other 2.714 r_mcangle_it 2.701 r_mcangle_other 2.701 r_scbond_it 1.588 r_scbond_other 1.588 r_mcbond_it 1.578 r_mcbond_other 1.577 r_angle_refined_deg 1.388 r_angle_other_deg 1.316 r_symmetry_xyhbond_nbd_refined 0.486 r_nbd_other 0.379 r_symmetry_nbd_refined 0.372 r_symmetry_xyhbond_nbd_other 0.245 r_nbd_refined 0.211 r_symmetry_nbd_other 0.21 r_xyhbond_nbd_other 0.208 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.169 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing