7BB2

Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 at 1.6A resolution (spacegroup P2(1)2(1)2(1))


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M D-Glucose, 0.1M D-Mannose, 0.1M D-Galactose, 0.1M L-Fucose, 0.1M D-Xylose, 0.1M N-Acetyl-D-Glucosamine, 0.1 M Imidazole/MES monohydrate (acid) pH 6.5, 20% v/v Ethylene glycol, 10 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5952.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.517α = 90
b = 100.028β = 90
c = 103.753γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.9716ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6103.751000.0960.99915.212.79330122.31
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.630.615

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-VALUE7ALH1.655.961.3493191463599.970.16540.16420.188631.96
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_d19.4985
f_angle_d0.9733
f_chiral_restr0.0514
f_bond_d0.0072
f_plane_restr0.0064
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4697
Nucleic Acid Atoms
Solvent Atoms588
Heterogen Atoms58

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing