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Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.75 293 100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (200 mM HEPES pH 7.75, 5% DMSO, 12.5% PEG4K).
Soaking: 200 mM HEPES pH 7.75, 12.5 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.
Crystal Properties Matthews coefficient Solvent content 1.99 38.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.539 α = 90 b = 53.602 β = 100.503 c = 44.57 γ = 90
Symmetry Space Group C 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 100 PIXEL DECTRIS EIGER X 16M 2020-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
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 1.6 48.4 99.3 0.055 0.065 0.035 0.999 15 6.6 34900
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 1.6 1.63 92.5 0.42 0.534 0.324 0.931 3.2 4.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7B2J 1.6 43.82 1.34 34876 1726 99.19 0.1708 0.1686 0.2138 0.2253 Random selection 27.61
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 17.6348 f_angle_d 1.1282 f_chiral_restr 0.0668 f_plane_restr 0.0087 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing