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Structure of SARS-CoV-2 Mpro mutant (T21I,S144A,T304I) in complex with Nirmatrelvir (PF-07321332)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Apo structure of the protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 0.1 M Tris, pH 8, 20 % 2-propanol, 5 % PEG8000
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.396 α = 90 b = 63.855 β = 90 c = 105.163 γ = 90
Symmetry Space Group P 21 21 2
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 9M 2022-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1 CLSI 08ID-1
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 1.54 41.68 78.4 0.998 9.8 5.5 36169
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 1.54 1.65 0.581
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.539 27.29 36162 1816 78.3 0.1966 0.1949 0.1885 0.229 0.2217 RANDOM 21.58
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] 0.0907 0.1099 -0.2006
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.22 t_omega_torsion 4.39 t_angle_deg 1.11 t_bond_d 0.01 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 35
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling