EMD-0160

Subtomogram averaging
8.9 Å
EMD-0160
3D View Gallery
Deposition: 31/07/2018
Map released: 26/09/2018
Last modified: 10/10/2018
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-0160
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
EMICSS annotations (xml)

Retromer-Vps5: map centred on the Vps26 dimer.

EMD-0160

Subtomogram averaging
8.9 Å
EMD-0160
3D View Gallery
Deposition: 31/07/2018
Map released: 26/09/2018
Last modified: 10/10/2018
Overview 3D View Sample Experiment Validation Additional data Links
Method: Subtomogram averaging
Aggregation State: 3D Array
Specimen preparation [1]
Concentration: 1.1 mg/mL
Details: The solution-assembled complex was incubated with Folch liposomes at room temperature.
Buffer
pH: 7.5
Buffer components [2]:
Name Formula Concentration ChEBI
HEPES-KOH C8H19KN2O5S 20.0 mM
Sodium chloride NaCl 200.0 mM
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 292 K
Instrument: LEICA EM GP
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: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 2.5 µm - 6.5 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
Number of grids: 2
Average electron dose per image: 3.17 e/Å2
Details: Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017)
Image processing [1]
Details: After motion correction in "alignframes" (IMOD), each of the images in the tilt series was low-pass filtered according to the electron-dose acquired by the sample (Grant and Grigorieff, 2015).
Final reconstruction
Resolution: 8.9 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Algorithm: BACK PROJECTION
Details:
⌯ Applied Symmetry
Point group: C2
⦩ Final angle assignment
Type: OTHER
Details: Image processing was performed in TOM Toolbox, AV3 and Dynamo toolboxes.
Software [2]
Name Version Details
AV3 - -
TOM - -
Extraction
Number of images used: 194885
Reference model: Reference-free
Method: Geometrical seeding alogn the surface of manually traced tubules
CTF correction
Details: CTF correction was performed with ctfphaseflip IMOD command using defocus values measured by CTFFIND4 on non-dose-filtered images.
Software [2]
Name Version Details
CTFFIND 4 -
IMOD - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Retromer-Vps5: map centred on the Vps26 dimer.
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 180 180 180
Dimensions (Å) 243.0 243.0 243.0
Voxel size (Å) 1.35 1.35 1.35
Contour list
Primary Level Source
True 0.15 AUTHOR