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- EMDB-51848: RuBisCo Average for EMPIAR-11830 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51848
TitleRuBisCo Average for EMPIAR-11830
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
KeywordsRuBisCo / PLANT PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 7.5 Å
AuthorsKhavnekar S
Funding support1 items
OrganizationGrant numberCountry
Max Planck Society
CitationJournal: To Be Published
Title: Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Authors: Khavnekar S
History
DepositionOct 18, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51848.png

Downloads & links

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Map

FileDownload / File: emd_51848.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 168 pix.
= 329.28 Å		1.96 Å/pix.
x 168 pix.
= 329.28 Å		1.96 Å/pix.
x 168 pix.
= 329.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-1.1086563 - 1.3259398
Average (Standard dev.)0.003432437 (±0.06600752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 329.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51848_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51848_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_51848_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 : Chlamydomonas reinhardtii

EntireName: Chlamydomonas reinhardtii (plant)
Components
  • Cell: Chlamydomonas reinhardtii

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Supramolecule #1: Chlamydomonas reinhardtii

SupramoleculeName: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number subtomograms used: 14000
ExtractionNumber tomograms: 14 / Number images used: 140000 / Method: STOPGAP / Software - Name: STOPGAP (ver. 0.7.3)
CTF correctionSoftware:
Namedetails
CTFFINDCTF estimated using tiltCTF estimation in TOMOMAN
NOVACTF

Details: CTF estimated using tiltCTF estimation in TOMOMAN / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 1 / Software - Name: STOPGAP (ver. 0.7.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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