EMD-2106 Experiments and Validation

HRV2 empty native capsid

Single particle reconstruction
Overview of EMD-2106
Sample name: HRV2 native empty particle
Organism: Human rhinovirus 2
Related EM entries by publication: EMD-2109, EMD-2108, EMD-2107

Map parameters

Minimum density: -2.76
Maximum density: 3.819
Average density: 0.075
Standard deviation: 0.501
Recommended contour level: 1.32 (author)

Sample information

Sample name: HRV2 native empty particle
Virus: Human rhinovirus 2

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: Xmipp
Number of particles: 2223
Reconstruction protocol: Projection Matching
CTF correction: Phase flipping & amplitude decay correction

Fitting

Initial atomic model: 1FPN
Used chains: 1, 2, 3, 4
Fitting software: URO
Fitting protocol: rigid body
Target criteria: CC
Refinement space: RECIPROCAL
Details: Protocol: Rigid body. The asymmetric unit was initially treated as a single rigid body and then refined, treating each subunit as an independent rigid body

Imaging

Session
Microscope model: FEI TECNAI F30
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Nominal CS (mm): 2.00
Nominal magnification: 71949.0
Defocus max (nm): 3,500.00
Defocus min (nm): 800.00
Holder model: PHILIPS ROTATION HOLDER
Acquisition
Number of images: 433
Sampling interval (μm): 15.0

Specimen

Preparation
Specimen state: particle
Buffer: 50 mM sodium borate
Staining procedure: Using a Leica EM Grid Plunger, sample was applied per grid in a humidified chamber, left for 30 s, blotted for 0.8 s and plunge-frozen
Specimen support: R 1.2/1.3 Quantifoil grids
Vitrification
Apparatus: LEICA EM GP
Cryogen: ETHANE
Humidity: 80