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- EMDB-51526: Human Transthyretin at 3.5A imaged on Falcon C -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51526
TitleHuman Transthyretin at 3.5A imaged on Falcon C
Map data
Sample
  • Complex: Transthyretin
KeywordsD2 symmetry / Tundra / Falcon C / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKoh FA / Karia D / Yang W / Yu L / Kotecha A / Lander GC
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: To Be Published
Title: Sub-3 A resolution structure determination using single-particle cryo-EM at 100 keV
Authors: Karia D / Koh A / Yang W / Cushing V / van der Ploeg R / Basanta B / Mihaylov D / Khavnekar S / Vyroubal O / Malinsky M / Shanel O / Dolezal V / Plitzko JM / Yu L / Lander GC / Aricescu R / Greber B / Kotecha A
History
DepositionSep 13, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51526.png

Downloads & links

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Map

FileDownload / File: emd_51526.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 96 pix.
= 125.76 Å		1.31 Å/pix.
x 96 pix.
= 125.76 Å		1.31 Å/pix.
x 96 pix.
= 125.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.52416265 - 0.5004204
Average (Standard dev.)0.00059340004 (±0.01956068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 125.759995 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51526_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_51526_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 : Transthyretin

EntireName: Transthyretin
Components
  • Complex: Transthyretin

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Supramolecule #1: Transthyretin

SupramoleculeName: Transthyretin / type: complex / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: OTHER / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.3 µm

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Image processing

DetailsFalcon C
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 131895
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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