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- EMDB-24887: 2.1 Angstrom resolution structure of Beta-galactosidase obtained ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-24887
Title2.1 Angstrom resolution structure of Beta-galactosidase obtained from Glacios equipped with Falcon 3
Map data
Sample
  • Complex: beta-galactosidase
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsMerk A / Darling JE / Grisshammer R / Ognjenovic J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: 2.1 Angstrom resolution structure of Beta-galactosidase obtained from Glacios equipped with Falcon 3
Authors: Merk A / Darling JE / Grisshammer R / Ognjenovic J
History
DepositionSep 16, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24887.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.26 Å/pix.
x 1200 pix.
= 315.6 Å
0.26 Å/pix.
x 1200 pix.
= 315.6 Å
0.26 Å/pix.
x 1200 pix.
= 315.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.263 Å
Density
Contour LevelBy AUTHOR: 0.0548
Minimum - Maximum-0.16232435 - 0.26757017
Average (Standard dev.)-6.4620144e-06 (±0.0062402925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120012001200
Spacing120012001200
CellA=B=C: 315.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24887_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_24887_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_24887_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : beta-galactosidase

EntireName: beta-galactosidase
Components
  • Complex: beta-galactosidase

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Supramolecule #1: beta-galactosidase

SupramoleculeName: beta-galactosidase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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 GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 217550

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