EMD-16032

Subtomogram averaging
1.6 Å
EMD-16032
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Deposition: 27/10/2022
Map released: 15/11/2023
Last modified: 15/11/2023
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-16032
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Structure of mouse heavy chain apoferritin solved by subtomogram averaging of 100 tilt series in Warp/M

EMD-16032

Subtomogram averaging
1.6 Å
EMD-16032
3D View Gallery
Deposition: 27/10/2022
Map released: 15/11/2023
Last modified: 15/11/2023
Overview 3D View Sample Experiment Validation Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Concentration: 5 mg/mL
Buffer
pH: 7.5
Buffer components [2]:
Name Formula Concentration ChEBI
4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid HEPES 20.0 mM
Sodium chloride NaCl 150.0 mM
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: TFS 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: 1.0 µm - 3.0 µm
Nominal magnification: 165000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Details: Tilt series acquired with Hagen scheme +-48 degrees with 3 increment
Specialist optics
Energy filter
Name: TFS Selectris X
Slit width: 10 eV
Image Recording [1]
Detector model: FEI FALCON IV (4k x 4k)
Dimensions: 4096 pixel x 4096 pixel
Number of grids: 1
Average exposure time: 0.5 s
Average electron dose per image: 3.5 e/Å2
Details: Imaged with TFS Selectris X and Falcon 4i
Image processing [1]
Final reconstruction
Resolution: 1.6 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: O
Software [1]
Name Version Details
Warp nb20201104 M
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
Warp nb20201104 M
Extraction
Number of images used: 31478
Method: Automatic 2D picking
Software [2]
Name Version Details
RELION 4 -
Warp nb20201104 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 384 384 384
Dimensions (Å) 279.93597 279.93597 279.93597
Voxel size (Å) 0.7289999 0.7289999 0.7289999
Contour list
Primary Level Source
True 0.0024 AUTHOR