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- EMDB-9865: The 1.54 A resolution structure of apoferritin by CRYOARM300 with... -

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Basic information

Entry
Database: EMDB / ID: EMD-9865
TitleThe 1.54 A resolution structure of apoferritin by CRYOARM300 with Cold-FEG
Map data
Sample
  • Complex: apoferritin
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.54 Å
AuthorsKato T / Nakane T / Makino F / Terahara N / Yonekura K / Namba K
CitationJournal: Microsc Microanal / Year: 2019
Title: CryoTEM with a Cold Field Emission Gun That Moves Structural Biology into a New Stage
Authors: Kato T / Makino F / Nakane T / Terahara N / Kaneko T / Shimizu Y / Motoki S / Ishikawa I / Yonekura K / Namba K
History
DepositionMar 25, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9865.png

Downloads & links

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Map

FileDownload / File: emd_9865.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 450 pix.
= 222.75 Å		0.5 Å/pix.
x 450 pix.
= 222.75 Å		0.5 Å/pix.
x 450 pix.
= 222.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.08164087 - 0.21387374
Average (Standard dev.)-0.00000260493 (±0.008363421)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 222.75 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.4950.4950.495
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z222.750222.750222.750
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0820.214-0.000

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Supplemental data

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Mask #1

Fileemd_9865_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: nominal 0.5 A/px, calibrated 0.495 A/px

Fileemd_9865_half_map_1.map
Annotationnominal 0.5 A/px, calibrated 0.495 A/px
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: nominal 0.5 A/px, calibrated 0.495 A/px

Fileemd_9865_half_map_2.map
Annotationnominal 0.5 A/px, calibrated 0.495 A/px
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : apoferritin

EntireName: apoferritin
Components
  • Complex: apoferritin

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Supramolecule #1: apoferritin

SupramoleculeName: apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 504 KDa

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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

Concentration4 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Both side glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
TemperatureMin: 100.4 K / Max: 100.4 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
DetailsJEM-Z300FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 947 / Average exposure time: 10.0 sec. / Average electron dose: 88.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.167 µm / Calibrated defocus min: 0.315 µm / Calibrated magnification: 101000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Startup modelType of model: INSILICO MODEL
In silico model: Insilico model was produced by "3D initial model" in RELION
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1dev) / Number images used: 120295
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1 dev)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1 dev)
FSC plot (resolution estimation)

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