6EUX

Structure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WSA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Crystals were obtained by mixing FluB double domain at 15 mg/ml in 50 mM Tris pH 7.5 and 10% glycerol and 5 mM of VX-787 with 0.1 M PTCP and 25% PEG1500.
Crystal Properties
Matthews coefficientSolvent content
2.4349.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.2α = 90
b = 73.2β = 90
c = 103.74γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2017-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.055099.70.1190.99710.465.720671
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1599.71.10.6441.755.78

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 REPLACEMENTTHROUGHOUT4WSA2.0540.1419649102299.710.230650.229450.25404RANDOM50.898
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]
11.6311.63-23.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.88
r_dihedral_angle_3_deg12.172
r_dihedral_angle_4_deg10.984
r_dihedral_angle_1_deg5.398
r_long_range_B_refined4.835
r_long_range_B_other4.715
r_mcangle_it2.517
r_mcangle_other2.516
r_scangle_other2.379
r_mcbond_it1.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.88
r_dihedral_angle_3_deg12.172
r_dihedral_angle_4_deg10.984
r_dihedral_angle_1_deg5.398
r_long_range_B_refined4.835
r_long_range_B_other4.715
r_mcangle_it2.517
r_mcangle_other2.516
r_scangle_other2.379
r_mcbond_it1.433
r_mcbond_other1.433
r_scbond_it1.351
r_scbond_other1.351
r_angle_refined_deg1.07
r_angle_other_deg0.835
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1792
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing