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- EMDB-0263: Horse spleen apo-ferritin with beam tilt correction in RELION-3.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-0263
TitleHorse spleen apo-ferritin with beam tilt correction in RELION-3.0
Map dataReconstruction calculated from images that were collected over 9 Quantifoil holes using beam shift instead of moving the stage, and then correct for beam tilt in RELION-3.0
Sample
  • Complex: Horse spleen apo-ferritin
    • Protein or peptide: horse spleen apo-ferritin
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
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.
History
DepositionSep 28, 2018-
Header (metadata) releaseDec 26, 2018-
Map releaseDec 26, 2018-
UpdateDec 26, 2018-
Current statusDec 26, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0263.png

Downloads & links

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Map

FileDownload / File: emd_0263.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction calculated from images that were collected over 9 Quantifoil holes using beam shift instead of moving the stage, and then correct for beam tilt in RELION-3.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0794664 - 0.17438789
Average (Standard dev.)-0.0002476701 (±0.009633977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0790.174-0.000

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Supplemental data

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Mask #1

Fileemd_0263_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Independently refined halfmap 2

Fileemd_0263_half_map_1.map
AnnotationIndependently refined halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Independently refined halfmap 1

Fileemd_0263_half_map_2.map
AnnotationIndependently refined halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Horse spleen apo-ferritin

EntireName: Horse spleen apo-ferritin
Components
  • Complex: Horse spleen apo-ferritin
    • Protein or peptide: horse spleen apo-ferritin

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Supramolecule #1: Horse spleen apo-ferritin

SupramoleculeName: Horse spleen apo-ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Equus caballus (horse)

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Macromolecule #1: horse spleen apo-ferritin

MacromoleculeName: horse spleen apo-ferritin / type: protein_or_peptide / ID: 1 / Details: Bought from Sigma / Enantiomer: DEXTRO
Source (natural)Organism: Equus caballus (horse)
SequenceString:
MSSQIRQNYS TEVEAAVNRL VNLYLRASYT YLSLGFYFDR DDVALEGVCH FFRELAEEKR EGAERLLKMQ NQRGGRALFQ DLQKPSQDEW GTTLDAMKAA IVLEKSLNQA LLDLHALGSA QADPHLCDFL ESHFLDEEVK LIKKMGDHLT NIQRLVGSQA GLGEYLFERL TLKHD

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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
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureBasic - Residual tilt: 1.2 mrad
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
DetailsUsed beam shift to collect data, corrected for beam tilt in RELION-3.0
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 450 / Average exposure time: 14.0 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.6 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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

Particle selectionNumber selected: 104992 / Details: Template-based auto-picking in RELION-3.0
CTF correctionSoftware - Name: RELION (ver. 3.0) / Details: In RELION reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 65131
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 100 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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