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- EMDB-9210: Rabbit muscle aldolase using (Topaz t0) - (published) picks -

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Basic information

Entry
Database: EMDB / ID: EMD-9210
TitleRabbit muscle aldolase using (Topaz t0) - (published) picks
Map dataCryosparc v0 with Topaz-published picks sharpened
Sample
  • Complex: Rabbit muscle aldolase
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsBepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B
CitationJournal: Res Comput Mol Biol / Year: 2018
Title: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.
Authors: Tristan Bepler / Andrew Morin / Alex J Noble / Julia Brasch / Lawrence Shapiro / Bonnie Berger /
History
DepositionOct 15, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 24, 2018-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9210.png

Downloads & links

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Map

FileDownload / File: emd_9210.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc v0 with Topaz-published picks sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-2.9271145 - 4.249481
Average (Standard dev.)-0.0014947427 (±0.15360367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.992212.992212.992
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.9274.249-0.001

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Supplemental data

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Mask #1

Fileemd_9210_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc v0 with Topaz-published picks unsharpened

Fileemd_9210_additional.map
AnnotationCryosparc v0 with Topaz-published picks unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryosparc v0 with Topaz-published picks half map

Fileemd_9210_half_map_1.map
AnnotationCryosparc v0 with Topaz-published picks half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryosparc v0 with Topaz-published picks half map

Fileemd_9210_half_map_2.map
AnnotationCryosparc v0 with Topaz-published picks half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit muscle aldolase

EntireName: Rabbit muscle aldolase
Components
  • Complex: Rabbit muscle aldolase

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Supramolecule #1: Rabbit muscle aldolase

SupramoleculeName: Rabbit muscle aldolase / type: complex / ID: 1 / Parent: 0 / Details: (Topaz t0) - (published) picks
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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
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) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Number grids imaged: 1 / Average exposure time: 6.0 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsCryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
Particle selectionNumber selected: 520533
Details: All initial particles were used in the final reconstruction; ie. no particle filtering or classification was performed.
Startup modelType of model: INSILICO MODEL / In silico model: Cryosparc v0 ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - Version: 0 / Number images used: 520533
Initial angle assignmentType: OTHER / Details: Cryosparc v0
Final angle assignmentType: OTHER / Details: Cryosparc v0

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