|Entry||Database: EMDB / ID: 5132|
|Title||The reconstructed F120 amyloid fibril represents the structure of a selected subpopulation from the Abeta(1-40) fibril sample with a mean crossover distance of 120 nm. The F140 subpopulation with a mean crossover distance of 140 nm had been studied and deposited previously (EMDB accession no. 5008).|
|Keywords||Alzheimer's disease / micromechanical properties / electron cryo-microscopy / amyloid fibrils|
|Sample||Human Abeta (1-40)|
|Source||Homo sapiens / human|
|Map data||Cross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm.|
|Method||helical reconstruction, at 10.1 Å resolution|
|Authors||Sachse C / Faendrich M / Grigorieff N|
|Citation||Angew. Chem. Int. Ed. Engl., 2010, 49, 1321-1323|
|Date||Deposition: Oct 10, 2009 / Header (metadata) release: Oct 12, 2009 / Map release: Oct 12, 2009 / Last update: Mar 2, 2016|
Downloads & links
|File||emd_5132.map.gz (map file in CCP4 format, 314 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.4 Å|
CCP4 map header:
-Entire Human Abeta (1-40)
|Entire||Name: Human Abeta (1-40) / Number of components: 1 / Oligomeric State: helical|
|Mass||Theoretical: 4.33 kDa|
-Component #1: protein, Abeta
|Protein||Name: Abeta / a.k.a: Abeta / Recombinant expression: No|
|Source||Species: Homo sapiens / human|
|Helical parameters||Axial symmetry: C2 (2 fold cyclic) / Hand: LEFT HANDED / Delta z: 4.8 Å|
|Sample solution||Specimen conc.: 1 mg/ml / Buffer solution: 50 mM Borate / pH: 8.7|
|Support film||Quantifoil 400 mesh 1.3 micrometer holes|
|Staining||Blot for 7 seconds before plunging|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77.2 K / Method: Blot for 7 seconds before plunging|
Details: Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K.
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Nov 9, 2005|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal), 58333 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1900 - 3500 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 93 K
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 62 / Scanner: ZEISS SCAI / Sampling size: 7 microns|
|Processing||Method: helical reconstruction|
Details: The fibrils in the sample were selected based on their uniform width. 2. The F120 subset of limited crossover distances (110-130 nm) was chosen for the reconstruction.
|3D reconstruction||Algorithm: iterative algebraic reconstruction|
Euler angles: one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps)
Software: SPIDER / CTF correction: Each particle CTFTILT / Resolution: 10.1 Å / Resolution method: 10.1
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