EMPIAR-12794 - Cryo-electron tomography on synaptic vesicles isolated from mouse brain (part 1) [multiple data sets in TIFF and MRC formats]

EMPIAR-12794

Cryo-electron tomography on synaptic vesicles isolated from mouse brain (part 1) [multiple data sets in TIFF and MRC formats]

Publication:

Molecular architecture of synaptic vesicles

Kravcenko U, Kudryashev M

Proceedings of the National Academy of Sciences 121 (2024)

PMID: 39602275

DOI: 10.1073/pnas.2407375121

Related EMDB entry:

EMD-18568 EMD-18557 EMD-18572 EMD-18578 EMD-18556

Deposited:

2025-01-27

Released:

2025-07-25

Last modified:

2025-07-25

Imageset size:

1.37 TB

Imageset DOI:

10.6019/EMPIAR-12794

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
tilt series
reconstructed volumes

Image Sets

1. Source unaligned micrographs (.tif) of synaptic vesicles isolated from mouse brain (part I)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.84, 0.84)

Details:

The naming correspondence between raw micrographs and tilt series/tomograms can be found in frames2tomos.txt.
The respective gain-reference file is SuperCDSRef_A_000_0.0.dm4
For this dataset raw micrographs were collected in 10 frames with a total dose per tilt view of 4.1391 e−/Å2 and the total dose distributed equally among all tilt images.
See top-level README.txt for contents location details.

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2. Source unaligned micrographs (.tif) of synaptic vesicles isolated from mouse brain (part II)

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.84, 0.84)

Details:

The naming correspondence between raw micrographs and tilt series/tomograms can be found in frames2tomos.txt.
The respective gain-reference file is SuperCDSRef_ts_051_000_-0.0.dm4
For this dataset raw micrographs were collected using high-dose zero-tilt scheme. Thus, a zero-tilt micrographs were collected in 75 frames with a total dose per image of 31.077 e−/Å2 and other tilt micrographs were collected in 10 frames with a total dose per image of 4.1391 e−/Å2.
See top-level README.txt for contents location details.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

3. Unaligned unbinned tilt stacks (.st) with metadata (.xf, .tlt, .defocus) of synaptic vesicles isolated from mouse brain

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.84, 0.84)

Details:

The metadata files could be used to align tilt stacks (.tlt and .xf), correct CTF (.defocus) and perform 3D reconstruction (.tlt), e.g. using IMOD.

Files:

This entry cannot be downloaded from PDBj.

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4. CTF-corrected binned tomograms (.rec) of synaptic vesicles isolated from mouse brain

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(512, 720)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.44, 13.44)

Details:

Particle coordinates and orientations could be found in the subfolder "/data/particle_tables/" of this deposition.
For additional info see file prtcls_description_dataset_1.txt

Files:

This entry cannot be downloaded from PDBj.

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