7SGU

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1 M sodium acetate pH 4.5, 2 M sodium formate, 4 mM PLP_Snyder608
Crystal Properties
Matthews coefficientSolvent content
3.8568.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.075α = 90
b = 85.075β = 90
c = 132.548γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-09-18MSINGLE 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
11.7942.571000.1110.1170.0350.9956.910.852971
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)
11.791.8299.71.691.8050.6260.5341.078.1

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 REPLACEMENTTHROUGHOUT6WRH1.7942.5750314261599.50.16810.16710.1877RANDOM45.221
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]
0.130.070.13-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.948
r_dihedral_angle_4_deg17.779
r_dihedral_angle_3_deg14.603
r_dihedral_angle_1_deg6.08
r_angle_refined_deg1.584
r_angle_other_deg1.511
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.948
r_dihedral_angle_4_deg17.779
r_dihedral_angle_3_deg14.603
r_dihedral_angle_1_deg6.08
r_angle_refined_deg1.584
r_angle_other_deg1.511
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.008
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2486
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms32

Software

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