7KRX

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441 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 pH 6.0, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder441
Crystal Properties
Matthews coefficientSolvent content
4.9975.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.333α = 90
b = 114.333β = 90
c = 219.573γ = 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
12.7249.851000.1730.1810.05216.312.420038
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)
12.722.7799.61.8441.9450.60.5430.9110

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 REPLACEMENTTHROUGHOUT6wrh2.7249.8518980103999.780.21190.20970.249RANDOM103.181
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]
3.843.84-7.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.183
r_dihedral_angle_4_deg21.779
r_dihedral_angle_3_deg16.447
r_dihedral_angle_1_deg7.738
r_angle_refined_deg1.881
r_angle_other_deg1.269
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.183
r_dihedral_angle_4_deg21.779
r_dihedral_angle_3_deg16.447
r_dihedral_angle_1_deg7.738
r_angle_refined_deg1.881
r_angle_other_deg1.269
r_chiral_restr0.073
r_bond_refined_d0.01
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 Atoms2445
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms42

Software

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