7XAR

Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.158 mM Nickel chloride 80 mM TRIS (pH 8.5) 16% PEG-MME 2,000 20% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2645.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.027α = 90
b = 63.362β = 90.4
c = 102.831γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
11.647.199.50.0590.99918.36.879374
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6398.60.8830.8152.27

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6Y2E1.647.0776114323899.390.17460.17320.2064RANDOM22.404
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]
-0.530.541.43-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.242
r_dihedral_angle_4_deg19.303
r_dihedral_angle_3_deg12.933
r_dihedral_angle_1_deg7.313
r_angle_refined_deg1.553
r_angle_other_deg1.439
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.242
r_dihedral_angle_4_deg19.303
r_dihedral_angle_3_deg12.933
r_dihedral_angle_1_deg7.313
r_angle_refined_deg1.553
r_angle_other_deg1.439
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4736
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing