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- EMDB-14348: 64K CDS Apoferritin map reconstructed from 32.5K sub-tomograms wi... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | 64K CDS Apoferritin map reconstructed from 32.5K sub-tomograms with emClarity | |||||||||
![]() | sharpened emClarity map | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / ![]() | |||||||||
![]() | Clare DK | |||||||||
Funding support | ![]()
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![]() | ![]() Title: 2.7 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER COMMISSIONING SESSION CM26464-2 USING SUB-TOMOGRAM AVERAGING Authors: Clare DK | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.6 KB 13.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.8 KB | Display | ![]() |
Images | ![]() | 296.8 KB | ||
Others | ![]() | 2.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened emClarity map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.356 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Relion sharpened emClarity/CisTEM map
File | emd_14348_additional_1.map | ||||||||||||
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Annotation | Relion sharpened emClarity/CisTEM map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : human Apoferritin
Entire | Name: human Apoferritin![]() |
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Components |
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-Supramolecule #1: human Apoferritin
Supramolecule | Name: human Apoferritin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 / Details: Heavy chain |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 500 KDa |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM TCEP |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time of 2.5 seconds. |
Details | The apoferritin sample was applied to in-house graphene-coated Quantifoil r2/2 EM grid |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Dose symmetric tilt series |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.5 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |