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- EMDB-0144: Human apo-ferritin reconstructed in RELION-3.0 -

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Basic information

Database: EMDB / ID: 0144
TitleHuman apo-ferritin reconstructed in RELION-3.0
Map dataHuman apo-ferritin reconstructed in RELION-3.0
Samplehuman apo-ferritin:
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 1.65 Å resolution
AuthorsZivanov J / Nakane T / Hagen WJH / Scheres SHW
CitationJournal: To be published
Title: RELION-3: new tools for automated high-resolution cryo-EM structure determination
Authors: Zivanov J / Nakane N / Forsberg B / Kimanius D / Hagen WJH / Lindahl E / Scheres SHW
DateDeposition: Jul 26, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Aug 8, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_0144.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
0.81 Å/pix.
= 293.04 Å
360 pix
0.81 Å/pix.
= 293.04 Å
360 pix
0.81 Å/pix.
= 293.04 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.016456531 - 0.06972927
Average (Standard dev.)0.00000443314 (0.0027883556)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 293.04 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8140.8140.814
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z293.040293.040293.040
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1270.3110.000

Supplemental data

Mask #1

Projections & Slices
Slices (1/2)
Density Histograms

Sample components

Entire human apo-ferritin

EntireName: human apo-ferritin / Number of components: 1

Component #1: protein, human apo-ferritin

ProteinName: human apo-ferritin / Recombinant expression: No
MassTheoretical: 440 kDa
SourceSpecies: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: Used beam shift to collect seven images within one 1.2um Quantifoil hole. Used active beamtilt compensation in TEM microscope software.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1255
Raw dataEMPIAR-10200 (Title: Human apo-ferritin reconstructed in RELION-3.0 / Data size: 191.5
Data #1: Unaligned multi-frame micrographs (in non-gain-corrected TIFF) of human apo-ferritin [micrographs - multiframe])

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 426450
3D reconstructionAlgorithm: FOURIER SPACE / CTF correction: In RELION reconstruction / Resolution: 1.65 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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