7OFU

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NFV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.
Crystal Properties
Matthews coefficientSolvent content
3.6866.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.391α = 90
b = 82.391β = 90
c = 134.132γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7248.9299.954116.6610.656596
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.7820.57610.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7nfv1.7248.86856588283499.9540.1760.17490.20233.774
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]
-0.073-0.037-0.0730.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.102
r_dihedral_angle_4_deg17.491
r_dihedral_angle_3_deg15.352
r_lrange_it7.346
r_lrange_other7.092
r_dihedral_angle_1_deg6.36
r_scangle_it5.45
r_scangle_other5.365
r_scbond_it3.708
r_scbond_other3.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.102
r_dihedral_angle_4_deg17.491
r_dihedral_angle_3_deg15.352
r_lrange_it7.346
r_lrange_other7.092
r_dihedral_angle_1_deg6.36
r_scangle_it5.45
r_scangle_other5.365
r_scbond_it3.708
r_scbond_other3.564
r_mcangle_it2.815
r_mcangle_other2.814
r_mcbond_it2.125
r_mcbond_other2.1
r_angle_refined_deg1.933
r_angle_other_deg1.534
r_symmetry_nbd_refined0.253
r_nbd_other0.221
r_nbd_refined0.218
r_xyhbond_nbd_refined0.212
r_nbtor_refined0.181
r_symmetry_xyhbond_nbd_refined0.178
r_symmetry_nbd_other0.177
r_symmetry_xyhbond_nbd_other0.13
r_chiral_restr0.099
r_symmetry_nbtor_other0.085
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2502
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing