6WZU

The crystal structure of Papain-Like Protease of SARS CoV-2 , P3221 space group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52770.1 M acetate buffer, 0.8 NaH2PO4/1.2 M K2HPO4, seeds from PLprotease C111S mutant crystals
Crystal Properties
Matthews coefficientSolvent content
3.6366.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.986α = 90
b = 81.986β = 90
c = 134.345γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-05-12MSINGLE 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
11.7948.841000.1370.1420.0376.614.249598
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)
11.791.831001.7811.8580.5230.6321.7212.4

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 REPLACEMENTTHROUGHOUT6WRH1.7948.8447056249899.790.16070.160.1741RANDOM36.074
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]
0.180.090.18-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.303
r_dihedral_angle_4_deg19.243
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg5.885
r_angle_refined_deg1.492
r_angle_other_deg1.421
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.303
r_dihedral_angle_4_deg19.243
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg5.885
r_angle_refined_deg1.492
r_angle_other_deg1.421
r_chiral_restr0.07
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 Atoms2502
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms25

Software

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