EMD-5590

Single-particle
12.7 Å
EMD-5590
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Deposition: 27/02/2013
Map released: 03/04/2013
Last modified: 06/11/2013
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5590
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

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

EMD-5590

Single-particle
12.7 Å
EMD-5590
3D View Gallery
Deposition: 27/02/2013
Map released: 03/04/2013
Last modified: 06/11/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Filament
Specimen preparation [1]
Concentration: 1 mg/mL
Buffer
pH: 2.0
Details: 10% acetonitrile/water solution
Grid
Details: Holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany)
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 99 K
Instrument: HOMEMADE PLUNGER
Method: Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature.
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal defocus: 0.9 µm - 3.0 µm
Nominal magnification: 40000.0
Calibrated magnification: 40000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification., Electron beam tilt params: )
Minimum tilt angle: 0
Maximum tilt angle: 0
Temperature
Minimum: 99 K
Average: 99 K
Maximum: 100 K
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: ZEISS SCAI
Number of real images: 250
Image processing [1]
Details: The particles were selected using an automatic selection program.
Final reconstruction
Resolution: 12.7 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 82
Algorithm: OTHER
Details:
⌯ Applied Symmetry
ΔΖ: 4.67 Å
ΔΦ: 0.85°
Software [1]
Name Version Details
SPIDER, IMAGIC, BKRP - -
Final 2D classification
Number of classes: 18
CTF correction
Details:CTFFIND3
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of doublet cross-beta amyloid fibril polymorph
Details: ::::EMDATABANK.org::::EMD-5590::::
⬡ Geometry
X Y Z
Dimensions 120 120 298
Origin -60 -59 -149
Spacing 120 120 298
Voxel size 1.8 Å 1.8 Å 1.7999998 Å
Contour list
Primary Level Source
True 230.43 AUTHOR