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- EMDB-29937: KLH1 Hemocyanin -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29937
TitleKLH1 Hemocyanin
Map dataKLH1 density map
Sample
  • Organelle or cellular component: Keyhole limpet hemocyanin 1
KeywordsCryo-TEM / Image reconstruction / OXYGEN BINDING
Biological speciesMegathura crenulata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSen A / Hosogi N / Brink J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: KLH1 Hemocyanin
Authors: Sen A / Hosogi N / Brink J
History
DepositionMar 2, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29937.png

Downloads & links

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Map

FileDownload / File: emd_29937.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKLH1 density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 400 pix.
= 521.48 Å		1.3 Å/pix.
x 400 pix.
= 521.48 Å		1.3 Å/pix.
x 400 pix.
= 521.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3037 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.7690406 - 3.1069672
Average (Standard dev.)0.0018938778 (±0.16411197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 521.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of KLH1

Fileemd_29937_half_map_1.map
AnnotationHalf map of KLH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of KLH1

Fileemd_29937_half_map_2.map
AnnotationHalf map of KLH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Keyhole limpet hemocyanin 1

EntireName: Keyhole limpet hemocyanin 1
Components
  • Organelle or cellular component: Keyhole limpet hemocyanin 1

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Supramolecule #1: Keyhole limpet hemocyanin 1

SupramoleculeName: Keyhole limpet hemocyanin 1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Megathura crenulata (invertebrata)

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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 / Chamber humidity: 85 % / Chamber temperature: 10 K

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 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: 0.1 µm

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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