6EUW

Crystal structure of the cap-binding domain of the PB2 subunit of influenza A/H5N1 polymerase bound to an azaindazole inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CB7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M di NaH phosphate and 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1643.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.49α = 90
b = 62.49β = 90
c = 69.97γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.0615ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1154.12940.0650.99612.614.4674557
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.0670.80.5080.8461.462.04

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 REPLACEMENTTHROUGHOUT4CB7154.1274557390793.980.140630.139450.16376RANDOM19.689
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]
0.270.140.27-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free31.36
r_dihedral_angle_2_deg27.719
r_dihedral_angle_4_deg13.613
r_dihedral_angle_3_deg12.954
r_sphericity_bonded9.502
r_dihedral_angle_1_deg5.839
r_long_range_B_other3.283
r_long_range_B_refined3.281
r_scangle_other2.728
r_scbond_it2.297
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free31.36
r_dihedral_angle_2_deg27.719
r_dihedral_angle_4_deg13.613
r_dihedral_angle_3_deg12.954
r_sphericity_bonded9.502
r_dihedral_angle_1_deg5.839
r_long_range_B_other3.283
r_long_range_B_refined3.281
r_scangle_other2.728
r_scbond_it2.297
r_scbond_other2.297
r_mcangle_it2.111
r_mcangle_other2.11
r_rigid_bond_restr1.675
r_angle_refined_deg1.587
r_mcbond_it1.575
r_mcbond_other1.553
r_angle_other_deg1.101
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1226
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing