7AU4

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.25293100 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 coefficientSolvent content
1.9536.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.828α = 90
b = 53.227β = 102.439
c = 44.59γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.976MAX IVBioMAX

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8255.5899.80.0560.0620.0270.9998.45.12345333.5
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)RedundancyNumber Unique Reflections (All)
11.821.8699.90.9621.0690.4610.7075.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7K3T1.8233.861.3423444115299.740.17680.17490.213940.41
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.422
f_angle_d1.0669
f_chiral_restr0.0621
f_bond_d0.0081
f_plane_restr0.0061
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms30

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction