EMD-10384 Experiments and Validation

A structure of the EIAV CA-SP hexamer (C6) from Gag-deltaMA spheres assembled at pH6

Subtomogram averaging
Overview of EMD-10384
Sample name: Equine infectious anemia virus
Organism: Equine infectious anemia virus
Fitted atomic model: 6t64
Related EM entries by publication: EMD-10381, EMD-10382, EMD-10383, EMD-10385, EMD-10386

Map parameters

Recommended contour level: 0.149 (author)
Number of grid points: 236 × 236 × 236
Voxel size: 1.04 × 1.04 × 1.04 Å
Minimum density: -0.286
Maximum density: 0.458
Average density: 0.007
Standard deviation: 0.053

Sample information

Sample name: Equine infectious anemia virus
Protein: Gag polyprotein
Virus: Equine infectious anemia virus

Validation information

Experimental information

 

Image processing

Applied symmetry: C6
Software: AV3, TOM Toolbox
Number of subtomograms averaged: 64961
CTF correction: CTF-correction was performed using NOVACTF

Fitting

Initial atomic model: 2EIA
Target criteria: Cross-correlation coefficient
Refinement space: REAL
Details: Rigid body fitting was done in Chimera. Missing residues were built de novo in Coot. Refinement was performed iteratively in Phenix and Coot.

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 3.3999999999999999
Energy filter: GIF Quantum LS
Nominal CS (mm): 2.70
Nominal magnification: 130000.0
Defocus max (nm): -3,500.00
Defocus min (nm): -1,500.00
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Details: nanoprobe
Acquisition
Details: Data was acquired using a dose-symmetric tilt acquisition scheme, as described in Hagen et al, 2017, J. Struct. Biol, 197(2):191-8

Specimen

Preparation
Specimen state: particle
Specimen support: 20 mA
Vitrification
Apparatus: FEI VITROBOT MARK II
Cryogen: ETHANE
Humidity: 90
Details: 1-2 seconds blot time, offset -3mm.