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Crystal Structure of SARS-CoV-2 Main Protease N142S 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, SITTING DROP 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 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.841 α = 90 b = 100.619 β = 90 c = 103.356 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 293 PIXEL DECTRIS PILATUS 2M 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRUS BEAMLINE MANACA 0.9772 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 1.845 56.313 39.62 0.949 4.4 4 24397
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 1.845 2.207 10.2 0.823 1.5
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 1.845 56.313 24393 1192 39.632 0.226 0.2242 0.2241 0.2654 0.2654 17.926
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] 0.536 0.203 -0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.53 r_dihedral_angle_4_deg 18.586 r_dihedral_angle_3_deg 16.447 r_dihedral_angle_1_deg 7.152 r_lrange_it 4.11 r_lrange_other 4.059 r_mcangle_other 2.077 r_mcangle_it 2.075 r_scangle_it 1.892 r_scangle_other 1.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.53 r_dihedral_angle_4_deg 18.586 r_dihedral_angle_3_deg 16.447 r_dihedral_angle_1_deg 7.152 r_lrange_it 4.11 r_lrange_other 4.059 r_mcangle_other 2.077 r_mcangle_it 2.075 r_scangle_it 1.892 r_scangle_other 1.892 r_angle_refined_deg 1.289 r_angle_other_deg 1.268 r_mcbond_it 1.172 r_mcbond_other 1.161 r_scbond_it 1.065 r_scbond_other 1.064 r_symmetry_xyhbond_nbd_refined 0.381 r_nbd_other 0.228 r_xyhbond_nbd_refined 0.226 r_symmetry_nbd_refined 0.218 r_symmetry_nbd_other 0.201 r_nbd_refined 0.192 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.157 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4732 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing