EMD-2397 Experiments and Validation

Cryo-EM reconstruction of enterovirus 71 in complex with a neutralizing antibody E18

Single particle reconstruction
Overview of EMD-2397
Sample name: Reconstruction of human enterovirus 71 in complex with Fab fragment of antibody E18
Organisms: Human enterovirus 71, Mus musculus
Fitted atomic model: 4c0u
Related EM entry by publication: EMD-2434, EMD-2436

Map parameters

Recommended contour level: 1.00 (author)
Number of grid points: 200 × 200 × 200
Voxel size: 2.48 × 2.48 × 2.48 Å
Minimum density: -4.858
Maximum density: 4.869
Average density: 0.023
Standard deviation: 0.918

Sample information

Sample name: Reconstruction of human enterovirus 71 in complex with Fab fragment of antibody E18
Protein: Fab EV18/4/D6-1/F1/G9
Virus: Human enterovirus 71

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: eman, eman2
Number of particles: 8335
Number of class averages: 122
Reconstruction protocol: projection matching
CTF correction: CTF determined for all particles from one film, phase flip

Fitting

Initial atomic model: 3ZFE
Used chains: A, B, C
Fitting software: EMFit
Fitting protocol: rigid body
Target criteria: Rcrit
Refinement space: REAL

Imaging

Session
Microscope model: FEI/PHILIPS CM200FEG
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 18.0
Nominal CS (mm): 2.00
Nominal magnification: 50000.0
Defocus max (nm): 4.50
Defocus min (nm): 0.75
Holder model: OTHER
Acquisition
Number of images: 112
Scanner model: NIKON SUPER COOLSCAN 9000

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 2.00
Buffer: 10 mM Tris-HCl, pH 8.0, 0.5 M NaCl, and 1 mM EDTA
Specimen support: Quantifoin R1.2/1.3 Holey carbon 200Mesh
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Humidity: 70
Protocol: Blot for 2 second before plunging