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The crystal structure of COVID-2019 main protease in the apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 0.1M HEPES sodium pH 7.5, 10% Propanol ,20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.88 α = 90 b = 102.34 β = 90 c = 103.49 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 100 CCD ADSC QUANTUM 315r 2020-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.91 72.77 99.9 0.049 13.9 13.1 743898 26.9734754348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.96 1.407
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 NONE 6LU7 1.91 72.77 1.34859193948 107878 3816 99.8454347725 0.221504456976 0.220077061897 0.2206 0.261688497256 0.2602 32.4808669861
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 16.8223029179 f_angle_d 0.887035610138 f_chiral_restr 0.0542323037488 f_bond_d 0.00809699431638 f_plane_restr 0.00603843014791
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4198 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing