6WRH

The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W9C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1 M Acetate buffer, 0.8 M NaH2PO4 / 1.2 M K2HPO4
Crystal Properties
Matthews coefficientSolvent content
3.6766.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.403α = 90
b = 82.403β = 90
c = 134.503γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-04-28MSINGLE 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)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
11.648.9999.10.0950.0980.0256.813.769708
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)
11.61.6389.50.8170.8710.2930.7411.718.3

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 REPLACEMENTTHROUGHOUT6W9C1.648.9966140351698.980.12550.12340.1643RANDOM28.527
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]
-0.07-0.03-0.070.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.188
r_dihedral_angle_4_deg17.253
r_dihedral_angle_3_deg12.88
r_dihedral_angle_1_deg6.017
r_rigid_bond_restr2.469
r_angle_refined_deg1.433
r_angle_other_deg1.427
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.188
r_dihedral_angle_4_deg17.253
r_dihedral_angle_3_deg12.88
r_dihedral_angle_1_deg6.017
r_rigid_bond_restr2.469
r_angle_refined_deg1.433
r_angle_other_deg1.427
r_chiral_restr0.071
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 Atoms2507
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms30

Software

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