EMD-5590 Experiments and Validation

Electron cryo-microscopy of a cross-beta amyloid fibril polymorph

Single particle reconstruction
Overview of EMD-5590
Sample name: Doublet cross-beta amyloid fibril polymorph
Organism: Rattus norvegicus
Fitted atomic model: 2m5k
Related EM entry by publication: EMD-2323, EMD-2324

Map parameters

Minimum density: -129.469
Maximum density: 860.173
Average density: 19.601
Standard deviation: 97.20
Recommended contour level: 230.43 (author)

Sample information

Sample name: Doublet cross-beta amyloid fibril polymorph
Protein: Transthyretin(105-115)

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: SPIDER, IMAGIC, BKRP
Number of particles: 82
Number of class averages: 18
Reconstruction protocol: Common crossovers
CTF correction: CTFFIND3

Imaging

Session
Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Nominal magnification: 40000.0
Defocus max (nm): 3,000.00
Defocus min (nm): 900.00
Tilt max (degrees): 0.00
Tilt min (degrees): 0.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 250
Scanner model: ZEISS SCAI

Specimen

Preparation
Specimen state: filament
Specimen concentration (mg/mL): 1.00
Buffer: 10% acetonitrile/water solution
Specimen support: holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany)
Aggregation parameters (helical parameters)
Handedness: LEFT HANDED
Phi increment (degrees): 0.84999999999999998
Azimuthal (Z) increment (Å): 4.6699999999999999
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Humidity: 95
Protocol: Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature.