7KOK

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder496 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62770.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder496
Crystal Properties
Matthews coefficientSolvent content
4.9375.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.554α = 90
b = 113.554β = 90
c = 219.682γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

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
1241.7699.90.1380.1410.030.9966.320.648260
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)
122.0399.11.7191.7840.460.614

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 REPLACEMENTTHROUGHOUT6wrh241.7645790244399.630.18540.1840.2106RANDOM61.067
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]
22-4.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.042
r_dihedral_angle_4_deg23.418
r_dihedral_angle_3_deg16.28
r_dihedral_angle_1_deg6.874
r_angle_refined_deg1.588
r_angle_other_deg1.311
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.042
r_dihedral_angle_4_deg23.418
r_dihedral_angle_3_deg16.28
r_dihedral_angle_1_deg6.874
r_angle_refined_deg1.588
r_angle_other_deg1.311
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2483
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms64

Software

Software
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing