EMD-3792

Tomography
EMD-3792
Gallery
Deposition: 10/07/2017
Map released: 16/08/2017
Last modified: 16/08/2017
Overview Sample Experiment Validation Additional data Links
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EMD-3792
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
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Electron cryotomogram of Vibrio cholerae O395 N1

EMD-3792

Tomography
EMD-3792
Gallery
Deposition: 10/07/2017
Map released: 16/08/2017
Last modified: 16/08/2017
Overview Sample Experiment Validation Additional data Links
Method: Tomography
Aggregation State: Cell
Specimen preparation [1]
Details: After 24 h of growth, the tube of V. cholerae culture was placed on a bench at room temperature for 1 min to sediment visible microcolonies. After the pellet was formed, the supernatant was gently removed by pipetting and the pellet was resuspended in fresh LB. The cells were incubated for 15 min prior to mixing with 10 nm colloidal gold.
Buffer
pH: 7.0
Buffer components [2]:
Name Formula Concentration ChEBI
Ampcillin C16H19N3O4S 100.0 ug/ml^-l
Isopropyl-B-D-thiogalactoside C9H18O5S 1.0 mM
Details: V. cholerae O395 N1 strains (wild-type or TCPM component knockout mutants) harbouring the pMT5-ToxT plasmid were grown in 5 ml lysogeny broth (LB) medium.
Grid
Mesh: 200
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Vitrification
Cryogen name: ETHANE-PROPANE
Fiducial Markers
Manufacturer Fiducial type Diameter
Sigma-Aldrich - 10 nanometer
Sectioning
Details: NO SECTIONING
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal defocus: 6.0 µm - 6.0 µm
Nominal magnification: 27500.0
Specimen holder model: OTHER
Specialist optics
Energy filter
Name: GIF
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Dimensions: 1856 pixel x 1918 pixel
Number of grids: 1
Average electron dose per image: 1.5 e/Å2
Image processing [1]
Final reconstruction
Number of images used: 121
Software [1]
Name Version Details
TOMO3D - SIRT reconstructions were then produced
CTF correction
Software [1]
Name Version Details
IMOD - -
Tomogram
Format: CCP4
Data type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
⬡ Geometry
X Y Z
Origin 0 0 800
Dimensions (px) 1856 1918 800
Dimensions (Å) 14476.801 14960.4 6240.0
Voxel size (Å) 7.8 7.8 7.8
Contour list
Primary Level Source
True - AUTHOR