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The structure of a Ty3 retrotransposon capsid C-terminal domain dimer
ELECTRON MICROSCOPY
Sample
Ty3 capsid C-terminal domain dimer
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
The sample was applied onto glow-discharged C-flat (Protochips Inc.) holey carbon grids. The grids were blotted from the back side for 11 seconds at r ...
The sample was applied onto glow-discharged C-flat (Protochips Inc.) holey carbon grids. The grids were blotted from the back side for 11 seconds at room temperature in a chamber at 85% humidity and plunge-frozen into liquid ethane using a manual plunger.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
74160
Reported Resolution (Å)
4.9
Resolution Method
FSC 0.143 CUT-OFF
Other Details
The Ty3 particles have a T=9 and each asymmetric unit of the lattice contains nine non-symmetry related Ty3 capsid protein monomers. We extracted all ...
The Ty3 particles have a T=9 and each asymmetric unit of the lattice contains nine non-symmetry related Ty3 capsid protein monomers. We extracted all non-symmetry related units from the final reconstructions from the two half datasets. The CA-CTDs were aligned and averaged separately. The final structure of the CA-CTD comes from nine averaged copies of the domain. The final structure of the CA-CTD was resolved at 4.9 A resolution at 0.143 FSC. Gaussian-smoothened ellipsoid-shaped masks were used for resolution measurements.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)
20
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
75000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Cryo-grids containing purified PR- Ty3 particles were imaged in a Titan Krios electron microscope equipped with a Falcon II direct electron detector, operated at 300 kV. Images were collected with a nominal magnification of 75000, giving a pixel size of 1.08 A. Images were collected in integrating mode with a total electron dose of 20 e/A2. The range of applied defocus values was between -1.0 um and -3.5 um.