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- EMDB-69194: Cryo-EM structure of Arabidopsis nucleosome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-69194
TitleCryo-EM structure of Arabidopsis nucleosome
Map data
Sample
  • Complex: Arabidopsis thaliana nucleosome reconstituted on Widom 601 DNA
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Probable histone H2A.1
    • Protein or peptide: Histone H2B.6
    • DNA: DNA(Widom 601)
    • DNA: DNA(Widom 601)
Keywordsnucleosome / NUCLEAR PROTEIN
Function / homology
Function and homology information


plant-type cell wall / chromocenter / chloroplast thylakoid / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / chloroplast stroma / plastid / chloroplast ...plant-type cell wall / chromocenter / chloroplast thylakoid / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / chloroplast stroma / plastid / chloroplast / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / peroxisome / chromatin organization / heterochromatin formation / protein heterodimerization activity / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A ...: / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B.6 / Histone H3.1 / Histone H4 / Probable histone H2A.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsHaga J / Takasuka TE
Funding support Japan, 1 items
OrganizationGrant numberCountry
Other privateG-2025-2-039 Japan
CitationJournal: To Be Published
Title: Structures of the Arabidopsis nucleosome and H3-H4 octasome assembled in a wheat germ cell-free co-expression chromatin assembly platform
Authors: Haga J / Banko P / Okimune K / Azuma T / Terashi G / Morishita R / Kita S / Maenaka K / Kihara D / Takasuka TE
History
DepositionFeb 14, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69194.png

Downloads & links

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Map

FileDownload / File: emd_69194.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.23587948 - 0.59107727
Average (Standard dev.)0.00050612626 (±0.01203343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69194_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69194_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_69194_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 : Arabidopsis thaliana nucleosome reconstituted on Widom 601 DNA

EntireName: Arabidopsis thaliana nucleosome reconstituted on Widom 601 DNA
Components
  • Complex: Arabidopsis thaliana nucleosome reconstituted on Widom 601 DNA
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Probable histone H2A.1
    • Protein or peptide: Histone H2B.6
    • DNA: DNA(Widom 601)
    • DNA: DNA(Widom 601)

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Supramolecule #1: Arabidopsis thaliana nucleosome reconstituted on Widom 601 DNA

SupramoleculeName: Arabidopsis thaliana nucleosome reconstituted on Widom 601 DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Col-0

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Col-0
Molecular weightTheoretical: 15.300968 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RFRPGTVALR EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VAALQEAAEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Col-o
Molecular weightTheoretical: 11.436467 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK IFLENVIRDA VTYTEHARRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Probable histone H2A.1

MacromoleculeName: Probable histone H2A.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Col-o
Molecular weightTheoretical: 13.95815 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MAGRGKTLGS GSAKKATTRS SKAGLQFPVG RIARFLKKGK YAERVGAGAP VYLAAVLEYL AAEVLELAGN AARDNKKTRI VPRHIQLAV RNDEELSKLL GDVTIANGGV MPNIHNLLLP KKTGASKPSA EDD

UniProtKB: Probable histone H2A.1

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Macromolecule #4: Histone H2B.6

MacromoleculeName: Histone H2B.6 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Col-o
Molecular weightTheoretical: 16.474459 KDa
Recombinant expressionOrganism: Triticum aestivum (bread wheat)
SequenceString:
MAPRAEKKPA EKKPAAEKPV EEKSKAEKAP AEKKPKAGKK LPKEAGAGGD KKKKMKKKSV ETYKIYIFKV LKQVHPDIGI SSKAMGIMN SFINDIFEKL ASESSKLARY NKKPTITSRE IQTAVRLVLP GELAKHAVSE GTKAVTKFTS S

UniProtKB: Histone H2B.6

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Macromolecule #5: DNA(Widom 601)

MacromoleculeName: DNA(Widom 601) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 171.477812 KDa
SequenceString: (DC)(DA)(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DT)(DA)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG) (DG)(DT)(DG)(DC)(DC)(DG) ...String:
(DC)(DA)(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DT)(DA)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG) (DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC) (DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DC)(DG) (DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DC) (DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT)(DA) (DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA) (DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT) (DG)(DT)(DG)(DC)(DT)(DT)(DC)(DT) (DG) (DA)(DT)(DG)(DG)(DA)(DA)(DC)(DT)(DG)(DG) (DA)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DT)(DA)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG) (DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT) (DC) (DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG) (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG) (DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG) (DC)(DT)(DG) (DT)(DC)(DC)(DC)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC) (DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC) (DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT) (DA)(DT)(DA) (DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC) (DT)(DC)(DA)(DC)(DA)(DC)(DT) (DG)(DT) (DC)(DG)(DT)(DC)(DC)(DG)(DA)(DA)(DT)(DT) (DC)(DT)(DC)(DC)(DA)(DG)(DT)(DA) (DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA) (DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC) (DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG) (DG)(DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA) (DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DC)(DT)(DA)(DA) (DG)(DA)(DG)(DC)(DA)(DG) (DT)(DT)(DA) (DT)(DC)(DT)(DA)(DG)(DA)(DA)(DT)(DA)(DG) (DC)(DC)(DA)(DC)(DC)

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Macromolecule #6: DNA(Widom 601)

MacromoleculeName: DNA(Widom 601) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 173.243844 KDa
SequenceString: (DG)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DT) (DC)(DT)(DA)(DG)(DA)(DT)(DA)(DA)(DC)(DT) (DG)(DC)(DT)(DC)(DT)(DT)(DA)(DG)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String:
(DG)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DT) (DC)(DT)(DA)(DG)(DA)(DT)(DA)(DA)(DC)(DT) (DG)(DC)(DT)(DC)(DT)(DT)(DA)(DG)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC) (DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA) (DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC) (DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC) (DT)(DC)(DC)(DA)(DG)(DG)(DT)(DA) (DC) (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DT)(DC) (DC)(DA)(DG)(DT)(DT)(DC)(DC)(DA)(DT) (DC)(DA)(DG)(DA)(DA)(DG)(DC)(DA)(DC)(DA) (DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT) (DG)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG)(DA) (DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DT)(DA)(DC)(DT)(DG) (DG)(DA) (DG)(DA)(DA)(DT)(DT)(DC)(DG)(DG)(DA)(DC) (DG)(DA)(DC)(DA)(DG)(DT)(DG)(DT) (DG) (DA)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG) (DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG) (DC)(DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG) (DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DA) (DC)(DT)(DG)(DG)(DA)(DG) (DA)(DA)(DT) (DT)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DA)(DT) (DC)(DC)(DT)(DT)(DG)

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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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average exposure time: 2.5 sec. / Average electron dose: 49.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8j91

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.1) / Number images used: 469637
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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