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- EMDB-51540: Adeno-associated Virus 9 at 2.8A imaged on Falcon C -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-51540
TitleAdeno-associated Virus 9 at 2.8A imaged on Falcon C
Map data
Sample
  • Virus: Adeno-associated virus 9
KeywordsI symmetry / Tundra / Falcon C / VIRUS
Biological speciesAdeno-associated virus 9
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKoh FA / Karia D / Yang W / Yu L / Kotecha A
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_51540.png

Downloads & links

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Map

FileDownload / File: emd_51540.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 280 pix.
= 359.8 Å		1.29 Å/pix.
x 280 pix.
= 359.8 Å		1.29 Å/pix.
x 280 pix.
= 359.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.08669228 - 0.16165227
Average (Standard dev.)0.0011286921 (±0.011078056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 359.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51540_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_51540_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 : Adeno-associated virus 9

EntireName: Adeno-associated virus 9
Components
  • Virus: Adeno-associated virus 9

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Supramolecule #1: Adeno-associated virus 9

SupramoleculeName: Adeno-associated virus 9 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 235455 / Sci species name: Adeno-associated virus 9 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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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: 7.2
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: 0.6 µm / Nominal defocus min: 0.2 µm

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Image processing

DetailsFalcon C
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 89673
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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