EMD-5495 Experiments and Validation

Cryo-EM reconstruction of Sputnik virus

Single particle reconstruction
Overview of EMD-5495
Sample name: Sputnik
Organism: Sputnik virophage
Fitted atomic model: 3j26
Related EM entry by publication: EMD-5496

Map parameters

Recommended contour level: 2.00 (author)
Number of grid points: 768 × 768 × 384
Voxel size: 1.10 × 1.10 × 1.10 Å
Minimum density: -2.144
Maximum density: 21.70
Average density: 0.109
Standard deviation: 1.242

Sample information

Sample name: Sputnik
Virus: Sputnik virophage

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: EMAN, Frealign
Number of particles: 12000
Reconstruction protocol: Projection matching
CTF correction: each particle

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 22.0
Nominal CS (mm): 2.70
Nominal magnification: 59000.0
Defocus max (nm): 2,400.00
Defocus min (nm): 1,100.00
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Acquisition
Scanner model: NIKON SUPER COOLSCAN 9000
Sampling interval (μm): 6.3499999999999996

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 1.00
Buffer: PBS
Specimen support: 400 mesh Cu grid (c-flat), 1.2 um hole, glow discharged
Vitrification
Apparatus: GATAN CRYOPLUNGE 3
Cryogen: ETHANE
Humidity: 90
Protocol: blot 6 seconds