EMD-5466 Experiments and Validation

Cryo-electron microscopy reconstruction of the Enterovirus 71 empty capsid

Single particle reconstruction
Overview of EMD-5466
Sample name: Enterovirus 71 empty capsid
Organism: Human enterovirus 71
Fitted atomic model: 3j23
Related EM entry by publication: EMD-5465

Map parameters

Minimum density: -3.25
Maximum density: 6.04
Average density: 0
Standard deviation: 1
Recommended contour level: 1 (author)

Sample information

Sample name: Enterovirus 71 empty capsid
Virus: Human enterovirus 71

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: EMAN2, auto3DEM
Number of particles: 1931
Reconstruction protocol: Common Lines
CTF correction: auto3DEM
Details: A single data set was used for the reconstruction. These particles were selected individually.

Fitting

Initial atomic model: 3VBU
Used chains: A, B, C
Fitting software: Chimera, Situs
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: rigid body. The protomer was fit in Chimera, used to generate a full crystal map, then docked as a rigid body in Situs.

Imaging

Session
Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 15.0
Nominal CS (mm): 2
Nominal magnification: 50000.0
Defocus max (nm): 4,370
Defocus min (nm): 1,730
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 40
Scanner model: NIKON SUPER COOLSCAN 9000
Sampling interval (μm): 6.3499999999999996

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.1
Buffer: 10 mM Tris-HCl, 20 mM NaCl, 5 mM MgCl2
Specimen support: glow discharged holey carbon Quantifoil electron microscopy grids
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE-PROPANE MIXTURE
Humidity: 95