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

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Open data


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Basic information

Entry
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: Elife / Year: 2018
Title: New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Authors: Jasenko Zivanov / Takanori Nakane / Björn O Forsberg / Dari Kimanius / Wim Jh Hagen / Erik Lindahl / Sjors Hw Scheres
Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory ...Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous RELION versions.
DateDeposition: Jul 26, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Dec 26, 2018

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Structure visualization

Movie
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1270.3110.000

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Supplemental data

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Mask #1

Fileemd_0144_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire human apo-ferritin

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

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Component #1: protein, human apo-ferritin

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

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Experimental details

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Sample preparation

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

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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
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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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])

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Image processing

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

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