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Title:Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus
Authors:Veesler D, Ng TS, Sendamarai AK, Eilers BJ, Lawrence CM, Lok SM, Young MJ, Johnson JE, Fu CY
Sample:Mature Sulfolobus Turreted Icosahedral Virus
Method:Single particle reconstruction (4.5 angstroms resolution)
Red flagLatest update:2013-11-20
Sample
Sample name: Mature Sulfolobus Turreted Icosahedral Virus
Theoretical molecular weight of the sample: 75
Components:
ID Type Name Exp. MW (MDa) Theo. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1virusSulfolobus turreted icosahedral virus75Sulfolobus turreted icosahedral virus
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
3.5 mg/mL23 mM KH2PO4, 19 mM (NH4)2SO4, 1 mM MgSO4, 2 mM CaCl2glow-discharged C-flat holey carbon grids (CF-2/2-4C, Protochips)
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE%94 KHOMEMADE PLUNGER msVitrification carried out at room temperature
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm800 nm2500 nm102189FIELD EMISSION GUNFEI FALCON I (4k x 4k) mmObjective lens astigmatism was corrected at 103,000 times magnification

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Nitrogen cooledFEI TITAN KRIOS AUTOGRID HOLDER eV90 K K K mrad18 e/Å2Nanoprobe mode was used30-MAR-2011
Processing
Protocol:Projection matching
Software:Frealign
CTF correction:Each particle
Number of particles:8903
Imposed symmetry:I
Resolution by author:4.5 Å
Resolution method:FSC at 0.143 cut-off. The reported resolution is for the entire reconstruction. The resolution of the coat subunit region (B345) is estimated to 3.9 A using the same criterion.
Processing details:The final reconstruction was sharpened with a negative temperature factor of 400A2.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
878 μm/pixel
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
2BBD CNSRECIPROCALPositional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot.
4IL7 CNSRECIPROCALPositional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot. Only the N-terminal domain was refined using CNS (residues 3-134). The C-terminal domain (residues 135-222) was only rigid-body fit using Coot and an arbitrary B-factor value of 150 A2 was assigned to it.