7END

Crystal structure of SARS-CoV 3CLpro in complex with the non-covalent inhibitor WU-04


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UJ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.429310% 2-propanal, 0.1 M sodium citrate pH 5.4, 10% PEG 10,000
Crystal Properties
Matthews coefficientSolvent content
3.4163.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.496α = 90
b = 82.677β = 103.64
c = 107.454γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2020-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.541

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
11.9930.7699.460.12360.12950.038490.99733.16113123821.85
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)
11.992.06199.620.40760.43440.1490.8645.128.4

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-VALUE1uj11.9930.761.3431087147799.50.19930.19740.23725.99
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_d15.4767
f_angle_d0.6386
f_chiral_restr0.0434
f_plane_restr0.0049
f_bond_d0.0034
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2371
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms34

Software

Software
Software NamePurpose
CrysalisProdata collection
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing