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- EMDB-39364: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (Dee... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39364
TitleT cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)
Map data
Sample
  • Cell: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)
Keywordsreceptor / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXin W / Huang B / Chi X / Liu Y / Xu M / Zhang Y / Li X / Su Q / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)
Authors: Xin W / Huang B / Chi X / Liu Y / Xu M / Zhang Y / Li X / Su Q / Zhou Q
History
DepositionMar 4, 2024-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39364.png

Downloads & links

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Map

FileDownload / File: emd_39364.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 215.46 Å		1.08 Å/pix.
x 200 pix.
= 215.46 Å		1.08 Å/pix.
x 200 pix.
= 215.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.018112443 - 1.9417863
Average (Standard dev.)0.0012443565 (±0.021324258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 215.45999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39364_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39364_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (Dee...

EntireName: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)
Components
  • Cell: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)

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Supramolecule #1: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (Dee...

SupramoleculeName: T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A (DeepEMhancer)
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 294780
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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