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Crystal Structure of SARS CoV-2 Mpro mutant L50F with Nirmatrelvir captured in two conformational states
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L0D 7L0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 10-20 % (w/v) PEG 3350, 0.20-0.30 M NaCl, and 0.1 M Bis-Tris methane pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.129 α = 90 b = 63.693 β = 90 c = 105.323 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 RIGAKU HyPix-6000HE 2022-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 25.41 99.82 0.08596 0.1216 0.08696 0.988 7.25 2 16012 17.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.279 99.55 0.3643 0.5152 0.3643 0.707 1.95 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7L0D 2.2 25.41 1.35 16012 801 99.93 0.1985 0.1955 0.2538 0.2239 17.67
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.6053 f_angle_d 1.0736 f_chiral_restr 0.0487 f_bond_d 0.0038 f_plane_restr 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2330 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 49
Software Software Software Name Purpose Coot model building PHENIX refinement PHASER phasing CrysalisPro data reduction CrysalisPro data scaling CrysalisPro data collection