EMD-2438

Subtomogram averaging
64.0 Å
EMD-2438 Deposition: 13/08/2013
Map released: 02/10/2013
Last modified: 16/10/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2438

Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery

EMD-2438

Subtomogram averaging
64.0 Å
EMD-2438 Deposition: 13/08/2013
Map released: 02/10/2013
Last modified: 16/10/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.6 mg/mL
Buffer
pH: 7.2
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
Microscopy [1]
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: )
Temperature
Minimum: 80 K
Average: 99 K
Maximum: 105 K
Specialist optics
Energy filter
Name: In-column Omega filter
Lower energy threshold: 10.0 eV
Upper energy threshold: 30.0 eV
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
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-64 ° 64 ° - - - - -
Image processing [1]
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:
Applied Symmetry
Point group: C1
Software [1]
Name Version Details
IMOD, Dynamo - -
Map
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::::
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