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Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-199)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 283 18-21% PEG3350, 0.1 M Bis-Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.341 α = 90 b = 63.087 β = 90 c = 121.349 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 EIGER R 4M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.25 53.34 99.7 0.137 0.952 11.05 7 20094
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 99.6 0.827 0.798 0.99 7.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2QCY 2.25 28.7 1.34 20035 982 99.73 0.2065 0.2043 0.2043 0.2502 0.2506 random
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 13.833 f_angle_d 0.677 f_chiral_restr 0.047 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2814 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing