EMD-2382 Experiments and Validation

The structure and super-organization of acetylcholine receptor-rapsyn complexes; class D

Subtomogram averaging
Overview of EMD-2382
Sample name: Postsynaptic membrane isolated from Torpedo marmorata electric organ
Organism: Torpedo marmorata
Fitted atomic model: 4bor
Related EM entries by publication: EMD-2381, EMD-2376, EMD-2377, EMD-2378, EMD-2383

Map parameters

Minimum density: -0.771
Maximum density: 1.112
Average density: 0.00
Standard deviation: 0.067
Recommended contour level: 0.278 (author)

Sample information

Sample name: Postsynaptic membrane isolated from Torpedo marmorata electric organ
Proteins: nicotinic acetylcholine receptor, Rapsyn

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: XMIPP, ML, TOMO
Number of subtomograms averaged: 3564
Number of class averages: 5
Reconstruction protocol: Maximum-likelihood subtomogram averaging

Fitting

Initial atomic model: 2BG9
Used chains: A, B, C, D, E
Fitting software: Chimera
Fitting protocol: rigid body
Refinement space: REAL

Imaging

Session
Microscope model: FEI POLARA 300
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 50.0
Energy filter: Gatan
Energy window (eV): 0.00
Nominal CS (mm): 2.00
Nominal magnification: 69000.0
Defocus max (nm): 6,000.00
Defocus min (nm): 3,000.00
Tilt max (degrees): 70.00
Tilt min (degrees): -70.00
Holder model: GATAN LIQUID NITROGEN
Details: dual tilt axis tomography
Acquisition
Number of images: 142
Sampling interval (μm): 15.0
Details: dual axis tilt series

Specimen

Preparation
Specimen state: particle
Buffer: 400 mM NaCl, 20 mM phosphate buffer, leupeptin 0.3 mg/l, pepstatin 1 mg/l
Staining procedure: unstained
Specimen support: 300 mesh copper grid with lacy carbon support, glow discharged in amylamine atmosphere
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Humidity: 90
Protocol: blot from the carbon side