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Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 BIS-TRIS pH=6.5, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.83 α = 90 b = 53.89 β = 100.338 c = 113.588 γ = 90
Symmetry Space Group I 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 293 PIXEL DECTRIS EIGER R 4M 2020-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 27.94 94.8 0.031 0.99 10 3.2 23518 24.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 83.5 0.318 0.796 1.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6WQF 1.8 27.94 1.35 23503 1143 94.73 0.1608 0.1587 0.159 0.2019 0.2007 29.72
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 19.9714 f_angle_d 1.0898 f_chiral_restr 0.0606 f_bond_d 0.0091 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing