EMD-6003

Subtomogram averaging
EMD-6003
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Deposition: 29/07/2014
Map released: 06/08/2014
Last modified: 03/09/2014
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-6003
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Cryo-electron tomography of full-length glycoprotein from Ebola virus-like particles

EMD-6003

Subtomogram averaging
EMD-6003
3D View Gallery
Deposition: 29/07/2014
Map released: 06/08/2014
Last modified: 03/09/2014
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.4
Details: 130 mM NaCl, 20 mM HEPES, 10% sucrose
Grid
Details: 200 mesh Quantifoil Multi-A
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 77 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 6 seconds at 22 degrees C, 100% humidity, blot offset -2, plunge into an ethane slurry cooled by liquid nitrogen.
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal defocus: 2.5 µm - 2.5 µm
Nominal magnification: 34000.0
Specimen holder model: GATAN LIQUID NITROGEN
Temperature
Average: 81 K
Specialist optics
Energy filter
Name: GATAN GIF
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 37
Average electron dose per image: 150 e/Å2
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-60 ° 60 ° - - - - -
Image processing [1]
Details: Subtomogram density was selected using an automatic selection program.
Final reconstruction
Details:
⌯ Applied Symmetry
Point group: C3
Software [1]
Name Version Details
IMOD - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Molecular structure of Ebola VLP full-length glycoprotein trimer, including the mucin-like domain
Details: ::::EMDATABANK.org::::EMD-6003::::
⬡ Geometry
X Y Z
Dimensions 55 55 99
Origin 0 0 0
Spacing 55 55 99
Voxel size 4.1 Å 4.1 Å 4.1 Å
Contour list
Primary Level Source
True 0.217 AUTHOR