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- EMDB-34051: rT66 Hybrid-form -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-34051
TitlerT66 Hybrid-form
Map datarT66 Hybrid-form
Sample
  • Complex: rT66 Hybrid-form
KeywordsOrigami / scaffold / tetrahedron / RNA
Biological speciesInovirus M13
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsZhang K / Li S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: To Be Published
Title: 3D RNA-scaffolded wireframe origami
Authors: Parsons M / Allan M / Li S / Shepherd T / Ratanalert S / Zhang K / Pullen K / Chiu W / Rouskin S / Bathe M
History
DepositionAug 9, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34051.png

Downloads & links

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Map

FileDownload / File: emd_34051.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationrT66 Hybrid-form
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.76
Minimum - Maximum-0.2027279 - 1.6809431
Average (Standard dev.)0.034441944 (±0.1446948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions128128128
Spacing128128128
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34051_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_34051_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 : rT66 Hybrid-form

EntireName: rT66 Hybrid-form
Components
  • Complex: rT66 Hybrid-form

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Supramolecule #1: rT66 Hybrid-form

SupramoleculeName: rT66 Hybrid-form / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Inovirus M13

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.3) / Number images used: 2171
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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