8FWO

Crystal structure of SARS-CoV-2 papain-like protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5277100 mM Sodium acetate, 0.8 M Monosodium phosphate, 1.2 M Dipotassium hydrogen phosphate
Crystal Properties
Matthews coefficientSolvent content
3.6566.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.005α = 90
b = 83.005β = 90
c = 133.964γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2021-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRUS BEAMLINE MANACA0.977LNLS SIRUSMANACA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.844.6599.890.99912.7525014031.64
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)
11.81.8640.627

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-VALUE7CMD1.844.651.3350093245299.90.1830.18130.216839.19
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_d5.7389
f_angle_d1.4013
f_chiral_restr0.0923
f_bond_d0.0162
f_plane_restr0.0097
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2468
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms21

Software

Software
Software NamePurpose
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement