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

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Basic information

Database: EMDB / ID: 9210
TitleRabbit muscle aldolase using (Topaz t0) - (published) picks
Map dataCryosparc v0 with Topaz-published picks sharpened
SampleRabbit muscle aldolase:
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 2.63 Å resolution
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
DateDeposition: Oct 15, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 24, 2018 / Last update: Oct 24, 2018

Structure visualization

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

Downloads & links


Fileemd_9210.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
0.83 Å/pix.
= 212.992 Å
256 pix
0.83 Å/pix.
= 212.992 Å
256 pix
0.83 Å/pix.
= 212.992 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Contour Level:0.6 (by author), 0.6 (movie #1):
Minimum - Maximum-2.9271145 - 4.249481
Average (Standard dev.)-0.0014947427 (0.15360367)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 212.992 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-2.9274.249-0.001

Supplemental data

Mask #1

Projections & Slices
Slices (1/2)
Density Histograms

Sample components

Entire Rabbit muscle aldolase

EntireName: Rabbit muscle aldolase / Details: (Topaz t0) - (published) picks / Number of components: 1

Component #1: protein, Rabbit muscle aldolase

ProteinName: Rabbit muscle aldolase / Details: (Topaz t0) - (published) picks / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

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

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 520533
Details: CryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
3D reconstructionSoftware: cryoSPARC / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Cryosparc v0

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