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Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with nirmatrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1M MMT pH8.0, 25% w/vPEG 1500
Crystal Properties Matthews coefficient Solvent content 2 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.208 α = 90 b = 53.761 β = 101.585 c = 45.551 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2022-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
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 2.65 48.583 98.7 0.986 6 3.9 7973
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 2.72 2.86 0.327
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 NONE 2.65 48.583 7973 398 98.884 0.181 0.1765 0.184 0.258 0.2607 79.122
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] 4.402 3.017 -2.435 -2.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.096 r_dihedral_angle_3_deg 15.818 r_lrange_it 14.585 r_lrange_other 14.583 r_dihedral_angle_6_deg 14.253 r_dihedral_angle_other_3_deg 12.615 r_scangle_it 10.236 r_scangle_other 10.234 r_mcangle_it 9.619 r_mcangle_other 9.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.096 r_dihedral_angle_3_deg 15.818 r_lrange_it 14.585 r_lrange_other 14.583 r_dihedral_angle_6_deg 14.253 r_dihedral_angle_other_3_deg 12.615 r_scangle_it 10.236 r_scangle_other 10.234 r_mcangle_it 9.619 r_mcangle_other 9.616 r_dihedral_angle_1_deg 8.745 r_scbond_it 6.423 r_scbond_other 6.42 r_mcbond_it 6.298 r_mcbond_other 6.286 r_angle_refined_deg 1.373 r_angle_other_deg 0.49 r_nbd_refined 0.242 r_symmetry_nbd_other 0.214 r_nbd_other 0.211 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbd_refined 0.157 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.085 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing