6EVK

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue m7GTP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5281Bat influenza polymerase protein in 50 mM HEPES-NaOH, 500 mM NaCl, 5 % glycerol, 2 mM TCEP, pH = 7.5 was adjusted to a concentration of 10 mg per ml, mixed in a 1:1 ratio with vRNA, which was an equimolar mixture of nucleotides 1-16 from the 5 prime end and nucleotides 1-18 or 3-18 from the 3 prime end. Protein-RNA with the addition of 5 mM m7GTP was mixed with mother liquor containing 0.7-1.5 M sodium-potassium phosphate at pH 5.0
Crystal Properties
Matthews coefficientSolvent content
3.1961.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 269.34α = 90
b = 148.7β = 98.17
c = 88.51γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.979ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
12.95099.60.1020.1150.99810.754.6376144
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.9899.81.221.380.5971.084.65

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 REPLACEMENTTHROUGHOUT4WSB2.95072389375599.580.235920.233990.27294RANDOM115.697
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]
2.155.88-1.05-2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_3_deg15.486
r_dihedral_angle_4_deg12.907
r_long_range_B_refined10.233
r_long_range_B_other10.226
r_mcangle_it6.322
r_mcangle_other6.322
r_dihedral_angle_1_deg6.151
r_scangle_other5.847
r_mcbond_it3.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_3_deg15.486
r_dihedral_angle_4_deg12.907
r_long_range_B_refined10.233
r_long_range_B_other10.226
r_mcangle_it6.322
r_mcangle_other6.322
r_dihedral_angle_1_deg6.151
r_scangle_other5.847
r_mcbond_it3.789
r_mcbond_other3.786
r_scbond_it3.36
r_scbond_other3.339
r_angle_refined_deg1.139
r_angle_other_deg0.906
r_chiral_restr0.063
r_bond_refined_d0.008
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 Atoms17434
Nucleic Acid Atoms600
Solvent Atoms38
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing