EMD-4375

Subtomogram averaging
26.3 Å
EMD-4375
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Deposition: 16/04/2018
Map released: 27/06/2018
Last modified: 25/07/2018
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-4375
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EMICSS annotations (xml)

GEM subtomogram average obtained for yeast cells treated with rapamycin

EMD-4375

Subtomogram averaging
26.3 Å
EMD-4375
3D View Gallery
Deposition: 16/04/2018
Map released: 27/06/2018
Last modified: 25/07/2018
Overview 3D View Sample Experiment Validation Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Details: GEMs imaged in rapamycin-treated yeast cells thinned by focused ion beam milling
Buffer
pH: 7.0
Grid
Model: Quantifoil R2/1
Material: COPPER
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE-PROPANE
Instrument: FEI VITROBOT MARK IV
Details: 10 seconds blot time, blot force 10.
Microscopy [1]
Microscope: FEI TITAN KRIOS
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
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Average electron dose per image: 1.5 e/Å2
Image processing [1]
Final reconstruction
Resolution: 26.3 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: I
Software [1]
Name Version Details
RELION - -
⦩ Final angle assignment
Type: OTHER
Extraction
Number of images used: 74
Method: Template matching + visual inspection
Software [1]
Name Version Details
PyTom - -
CTF correction
Software [1]
Name Version Details
PyTom - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: GEM subtomogram average obtained for yeast cells treated with rapamycin
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 200 200 200
Dimensions (Å) 684.0 684.0 684.0
Voxel size (Å) 3.42 3.42 3.42
Contour list
Primary Level Source
True 0.1 AUTHOR