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Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 293 100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (100 mM Tris pH 8.25, 5% DMSO, 12.5% PEG4K).
Soaking: 100 mM Tris pH 8.25, 10 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.
Crystal Properties Matthews coefficient Solvent content 1.95 36.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.828 α = 90 b = 53.227 β = 102.439 c = 44.59 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 2020-10-08 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 1.82 55.58 99.8 0.056 0.062 0.027 0.999 8.4 5.1 23453 33.5
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 1.82 1.86 99.9 0.962 1.069 0.461 0.707 5.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K3T 1.82 33.86 1.34 23444 1152 99.74 0.1768 0.1749 0.1758 0.2139 0.2155 40.41
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 20.422 f_angle_d 1.0669 f_chiral_restr 0.0621 f_bond_d 0.0081 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction