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- EMDB-22030: Reprocessing of EMPIAR-10335 data (streptavidin) with particles p... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-22030
TitleReprocessing of EMPIAR-10335 data (streptavidin) with particles picked by Kpicker
Map data
Sample
  • Complex: Streptavidin
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsMcSweeney DM / McSweeney SM / Liu Q
CitationJournal: IUCrJ / Year: 2020
Title: A self-supervised workflow for particle picking in cryo-EM.
Authors: Donal M McSweeney / Sean M McSweeney / Qun Liu /
Abstract: High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an ...High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as , , , and .
History
DepositionMay 21, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22030.png

Downloads & links

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Map

FileDownload / File: emd_22030.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 128 pix.
= 137.216 Å		1.07 Å/pix.
x 128 pix.
= 137.216 Å		1.07 Å/pix.
x 128 pix.
= 137.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.24868038 - 0.36365741
Average (Standard dev.)0.00021926648 (±0.012127737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 137.216 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0721.0721.072
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z137.216137.216137.216
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2490.3640.000

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Supplemental data

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Sample components

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Entire : Streptavidin

EntireName: Streptavidin
Components
  • Complex: Streptavidin

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Supramolecule #1: Streptavidin

SupramoleculeName: Streptavidin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Streptomyces avidinii (bacteria)

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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: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12206
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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