EMD-4422

Tomography
EMD-4422
Gallery
Deposition: 14/11/2018
Map released: 05/12/2018
Last modified: 19/12/2018
Overview Sample Experiment Validation Additional data Links
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EMD-4422
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EMICSS annotations (xml)

Representative tomogram of immature MLV particles

EMD-4422

Tomography
EMD-4422
Gallery
Deposition: 14/11/2018
Map released: 05/12/2018
Last modified: 19/12/2018
Overview Sample Experiment Validation Additional data Links
Method: Tomography
Aggregation State: Particle
Specimen preparation [1]
Details: Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold.
Buffer
pH: 6.0
Grid
Mesh: 300
Model: C-flat-2/1
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 288 K
Instrument: FEI VITROBOT MARK II
Fiducial Markers
Manufacturer Fiducial type Diameter
UMC Utrecht - 10 nanometer
Sectioning
Details: NO SECTIONING
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 2.0 µm - 4.5 µm
Nominal magnification: 105000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: ZEMLIN TABLEAU
Specialist optics
Energy filter
Name: GIF Quantum LS
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 QUANTUM (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 3710 pixel x 3838 pixel
Sampling interval: 5.0 µm
Frames per image: 1-6
Number of grids: 1
Average exposure time: 0.6 s
Average electron dose per image: 2.5 e/Å2
Image processing [1]
Final reconstruction
Number of images used: 40
Software [1]
Name Version Details
ETomo - -
CTF correction
Software [2]
Name Version Details
MATLAB - CTF determination
IMOD - Phase flipping only
Tomogram
Format: CCP4
Data type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotation details: Representative tomogram of immature MLV particles for subtomogram averaging
⬡ Geometry
X Y Z
Origin -1 -1 -1
Dimensions (px) 1855 1855 810
Dimensions (Å) 5008.5 5008.5 2187.0
Voxel size (Å) 2.7 2.7 2.7
Contour list
Primary Level Source
True - AUTHOR