EMD-5563 Experiments and Validation

Electron microscopy of Everglades virus

Single particle reconstruction
Overview of EMD-5563
Sample name: Everglades virus
Organism: Everglades virus

Map parameters

Recommended contour level: 13.00 (emdb)
Number of grid points: 200 × 200 × 200
Voxel size: 4.00 × 4.00 × 4.00 Å
Minimum density: -72.682
Maximum density: 68.752
Average density: 0.00
Standard deviation: 9.224

Sample information

Sample name: Everglades virus
Virus: Everglades virus

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: IMAGIC-5
Number of particles: 1000
Reconstruction protocol: angular reconstitution
CTF correction: micrograph
Details: final maps were calculated from individual particles particles picked with EMAN2 boxer, reconstructed using IMAGIC-5

Imaging

Session
Microscope model: JEOL 2200FS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Energy filter: omega
Nominal CS (mm): 2.00
Nominal magnification: 60000.0
Defocus max (nm): 2,300.00
Defocus min (nm): 300.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 80
Sampling interval (μm): 15.0

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 1.00
Buffer: 0.05 M Tris HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA
Specimen support: C-flat 1.2/1.3 holey film
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Humidity: 60
Protocol: blot for 4 seconds before plunging