EMD-2438
Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery
EMD-2438
Subtomogram averaging64.0 Å
Deposition: 13/08/2013
Map released: 02/10/2013
Last modified: 16/10/2013
Concentration: 0.6
mg/mL
Buffer
pH: 7.2
Details: 20 mM Phosphate Buffer 1 mM MgCl2
Details: 20 mM Phosphate Buffer 1 mM MgCl2
Grid
Details: 200 mesh QUANTIFOIL R 2/1 (or R 3.5/1) copper grid, glow discharged in air atmosphere
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 120 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 4 seconds before plunging
Chamber humidity: 95%
Chamber temperature: 120 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 4 seconds before plunging
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 5.0 µm - 8.0 µm
Nominal magnification: 25000.0
Calibrated magnification: 34138.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 5.0 µm - 8.0 µm
Nominal magnification: 25000.0
Calibrated magnification: 34138.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification, Electron beam tilt params: )
Temperature
Minimum: 80
K
Average: 99 K
Maximum: 105 K
Average: 99 K
Maximum: 105 K
Specialist optics
Energy filter
Image Recording
[1]
Detector category:
FILM
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Scanner: OTHER
Average electron dose per image: 100 e/Å2
Bits per pixel: 16.0
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Scanner: OTHER
Average electron dose per image: 100 e/Å2
Bits per pixel: 16.0
Tilt Series
[1]
Axis 1 | Axis 2 | |||||
---|---|---|---|---|---|---|
Min. | Max. | Inc. | Min. | Max. | Inc. | Rotation |
-64 ° | 64 ° | - | - | - | - | - |
Details: The tube was use as pivot for initial alignment. Please see details in primary reference.
Final
reconstruction
Resolution: 64.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Algorithm: OTHER
Details:
Resolution method: FSC 0.5 CUT-OFF
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group:
C1
Software
[1]
Name | Version | Details |
---|---|---|
IMOD, Dynamo | - | - |
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
Details: ::::EMDATABANK.org::::EMD-2438::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Contour level in sigma as defined by the threshold level displayed by Chimera over the RMS of the map. The recommended contour level for the visualization of the internal vesicle is about 0.35 sigma
Details: ::::EMDATABANK.org::::EMD-2438::::
⬡ Geometry
X | Y | Z | |
---|---|---|---|
Dimensions | 96 | 96 | 96 |
Origin | 0 | 0 | 0 |
Spacing | 96 | 96 | 96 |
Voxel size | 8.8 Å | 8.8 Å | 8.8 Å |
Contour list
Primary | Level | Source |
---|---|---|
True | 1.5 | AUTHOR |