EMD-3977
Cryo-electron tomogram of the Chlamydomonas reinhardtii Golgi apparatus
EMD-3977
Tomography
Deposition: 07/11/2017Map released: 29/11/2017
Last modified: 29/11/2017
Details: The cells were frozen onto grids, then thinned using cryo-focused ion beam milling.
Buffer
pH: 7.0
Details: TAP media
Details: TAP media
Grid
Vitrification
Cryogen name: ETHANE-PROPANE
Chamber humidity: 90%
Instrument: FEI VITROBOT MARK IV
Details: Blotted from the back side for 10 seconds with 10 blot force before plunging.
Chamber humidity: 90%
Instrument: FEI VITROBOT MARK IV
Details: Blotted from the back side for 10 seconds with 10 blot force before plunging.
Sectioning (Focused ion beam)
Instrument:
OTHER
Ion: OTHER
Voltage: 30 kV
Current: 0.03 nA
Dose rate: 2 ions/(cm^2*s)
Duration: 2400 s
Temperature: 80 K
Initial thickness: 5000 nm
Final thickness: 240 nm
Details: Starting curent: 0.5 nA, Final current: 0.03 nA. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Scios DB-FIB. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.
Ion: OTHER
Voltage: 30 kV
Current: 0.03 nA
Dose rate: 2 ions/(cm^2*s)
Duration: 2400 s
Temperature: 80 K
Initial thickness: 5000 nm
Final thickness: 240 nm
Details: Starting curent: 0.5 nA, Final current: 0.03 nA. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Scios DB-FIB. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 4.0 µm - 6.0 µm
Nominal magnification: 42000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 4.0 µm - 6.0 µm
Nominal magnification: 42000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Specialist optics
Energy filter
Image Recording
[1]
Detector model:
GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Frames per image: 1-12
Average exposure time: 1.5 s
Average electron dose per image: 1.5 e/Å2
Detector mode: COUNTING
Frames per image: 1-12
Average exposure time: 1.5 s
Average electron dose per image: 1.5 e/Å2
Format: CCP4
Data type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotation details: Cryo-electron tomogram of Chlamydomonas reinhardtii Golgi apparatus
Data type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotation details: Cryo-electron tomogram of Chlamydomonas reinhardtii Golgi apparatus
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Origin | 0 | 0 | 68 |
| Dimensions (px) | 928 | 928 | 464 |
| Dimensions (Å) | 12695.04 | 12695.04 | 6347.52 |
| Voxel size (Å) | 13.68 | 13.68 | 13.68 |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | - | AUTHOR |