EMD-2296 Experiments and Validation

The 14 A Cryo-EM structure of Dengue virus at 37C

Single particle reconstruction
Overview of EMD-2296
Sample name: Dengue Virus 2
Organism: Dengue virus 2
Fitted atomic model: 3zko

Map parameters

Recommended contour level: 2.00 (author)
Number of grid points: 500 × 500 × 500
Voxel size: 1.90 × 1.90 × 1.90 Å
Minimum density: -6.129
Maximum density: 10.113
Average density: 0.036
Standard deviation: 0.992

Sample information

Sample name: Dengue Virus 2
Virus: Dengue virus 2

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: EMAN, EMAN2, MPSA
Number of particles: 5861
Reconstruction protocol: Cross-common lines
CTF correction: Each particle
Details: The particles were selected manually. The particles were selected manually

Fitting

Initial atomic model: 1P58
Used chains: A, B, C
Fitting software: Chimera
Fitting protocol: rigid body
Target criteria: Correlation
Refinement space: REAL
Details: Individual envelope protein molecules were fitted separately by manual docking using program O

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 18.5
Nominal CS (mm): 2.70
Nominal magnification: 47000.0
Defocus max (nm): 3,000.00
Defocus min (nm): 1,500.00
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Acquisition
Number of images: 302

Specimen

Preparation
Specimen state: particle
Buffer: 10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
Specimen support: lacey carbon grid, layered with ultra thin carbon
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Protocol: 2.5 microlitres virus sample was added per grid and blotted with filter paper for 2.5 s before plunging