EMD-2060 Experiments and Validation

Cryo-EM structure of HBV T=4 empty Cp183 capsid

Single particle reconstruction
Overview of EMD-2060
Sample name: HBV T=4 pgRNA-filled Cp183-EEE capsid
Organism: Hepatitis B virus
Related EM entries by publication: EMD-2059, EMD-2058, EMD-2057

Map parameters

Minimum density: -75.32
Maximum density: 132.83
Average density: 0.005
Standard deviation: 19.996
Recommended contour level: 35.00 (author)

Sample information

Sample name: HBV T=4 pgRNA-filled Cp183-EEE capsid
Virus: Hepatitis B virus

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: Auto3dem
Number of particles: 7439
CTF correction: Each particle phase-flipping

Imaging

Session 1
Microscope model: JEOL 3200FS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 14.0
Energy filter: Omega filter
Nominal CS (mm): 1.10
Nominal magnification: 80000.0
Defocus max (nm): 4,870.00
Defocus min (nm): 540.00
Holder model: GATAN LIQUID NITROGEN
Session 2
Microscope model: JEOL 3200FS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 14.0
Energy filter: Omega filter
Nominal CS (mm): 1.10
Nominal magnification: 80000.0
Defocus max (nm): 4,870.00
Defocus min (nm): 540.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 394

Specimen

Preparation
Specimen state: particle
Buffer: 150mM NaCl, 50mM Tris, 2mM DTT
Specimen support: Quantifoil R 2/2 holey carbon 200 mesh copper grids
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 4 seconds before plunging