EMPIAR-11078 - In situ cryo-electron tomography of the C. reinhardtii ciliary transition zone [multiple data sets in MRC and EM formats]

EMPIAR-11078

In situ cryo-electron tomography of the C. reinhardtii ciliary transition zone [multiple data sets in MRC and EM formats]

Publication:

In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains

van den Hoek H, Klena N, Jordan MA, Alvarez Viar G, Righetto RD, Schaffer M, Erdmann PS, Wan W, Geimer S, Plitzko JM, Baumeister W, Pigino G, Hamel V, Guichard P, Engel BD

Science (New York, N.Y.) 377 (2022) 543-548

PMID: 35901159

DOI: 10.1126/science.abm6704

Related EMDB entry:

EMD-15262

Deposited:

2022-06-23

Released:

2022-08-12

Last modified:

2022-08-12

Imageset size:

302.04 GB

Imageset DOI:

10.6019/EMPIAR-11078

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
subtomograms
tilt series
micrographs - multiframe

Image Sets

1. Deconvoluted bin4 tomograms for visualization

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(13.68, 13.68)

Details:

Volumes reconstructed in IMOD were deconvoluted using tom_deconv.m:
https://github.com/dtegunov/tom_deconv/blob/master/tom_deconv.m

Files:

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

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

2. CTF-corrected bin4 tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(13.68, 13.68)

Details:

Volumes reconstructed in IMOD at bin4 using phase-flipping for CTF correction.

Files:

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. CTF-corrected bin2 tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1856, 1856)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(6.84, 6.84)

Details:

Volumes reconstructed in IMOD at bin2 using phase-flipping for CTF correction.

Files:

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)

4. Subtomograms at bin2

Category:

subtomograms

Image format:

No. of images or tilt series:

2923

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(6.84, 6.84)

Details:

Subtomograms extracted from bin2 tomograms used in alignments and averaging. Each sub-directory contains the particles for a specific structure, namely:
A/ (IFT-A)
B/ (IFT-B)
D/ (IFT-Dynein 1b)
MTD-MIP/
Sleeve/
Stellate/
Y-link/

Files:

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)

5. Aligned tilt series stacks

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(13.68, 13.68)

Details:

Drift-corrected, aligned tilt series for each tomogram in a single stack (.ali extension from IMOD)

Files:

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)

6. Unaligned tilt series raw frames

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.42, 3.42)

Details:

Raw frames from Titan Krios (300 kV, Cs 2.7 mm) equipped with K2 direct electron detector in counting mode and energy filter. The number of frames is variable. In each of the 20 tomogram folders (Tomo1-Tomo20), there is:
Aligned tilt series (.ali file)
raw_data/imod_metadata/ (.defocus, .tlt and .xf metadata files for reconstruction in IMOD)
raw_data/mdocs/ (.mdoc files from SerialEM with data collection information)
raw_data/raw_frames/ (raw frames for individual tilts in MRC format, compressed with bzip2)

Files:

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)

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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

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