EMPIAR-11580 - Molecular model of a bacterial flagellar motor in situ reveals a “parts-list” of protein adaptations to increase torque [multiple data sets in MRC format]

EMPIAR-11580

Molecular model of a bacterial flagellar motor in situ reveals a “parts-list” of protein adaptations to increase torque [multiple data sets in MRC format]

Publication:

Molecular model of a bacterial flagellar motor in situ reveals a “parts-list” of protein adaptations to increase torque

Beeby M, Drobnič T

(---)

Related EMDB entry:

Deposited:

2023-02-03

Released:

2024-08-26

Last modified:

2024-08-26

Imageset size:

10.09 TB

Imageset DOI:

10.6019/EMPIAR-11580

Experimental metadata:

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Compressed by PDBj:

Image formats and pixel types shown below are those of the original, non-compressed files.

MRC movies (BigKahuna/Movies/*/Images-Disc1/GridSquare_*/Data/*.mrc) in this entry were compressed
by bzip2 (pbzip2) by EMPIAR Japan to save space and bandwidth.

The K2 dataset contained the same number of gain reference files (*-gain-ref.MRC) as the movies but
they were all identical. Thus, we moved one of them as
BigKahuna/Movies/2020-10-01_K2_dataset/Images-Disc1/gain-reference.mrc 
and deleted all the others.

Some programs (e.g. RELION >= 4.0.1 and CryoSPARC) can process compressed movies without explicit
decompression. For other programs, movies have to be decompressed beforehand. In this case,
you might want to convert decompressed MRC movies into TIFF to save your local storage.

Original size:   24,403,860,327 kilobytes
Compressed size:  7,866,768,128 kilobytes

Contains:

micrographs - multiframe

Image Sets

1. Dataset 2 (“K2”)

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

43006

Image size:

(3838, 3710)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(2.2, 2.2)

Details:

Campylobacter_K2_20201001_151628_EPU

64,000 np EFTEM
2.2 A/pix
20eV slit
Spot 7
1.50 um beam size
17 s exp
32 frames
Dose rate: 14 e/p/s, 2.89 e/A2/s
50 e/A2 total dose
1.53 e/A2/frame
-1.5 um to -3.0 um defocus
Autofocus at 105,000 nP (1.05 um beam size)
0.6/1 quantifoil grids
To detect holes in EPU, use 9mm defocus in GridSq mode and "allow dark holes"
One shot per hole

Files:

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

2. Dataset 1 (“F3”)

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

8775

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.748, 1.748)

Details:

campylobacter_mini_20200611_131510_EPU

47,000 nP
1.75 A/pix
50um C2
100um obj
spot 4
beam size: 1.3um
defocus range: -1.5 to -3.0
1.02 s exposure
10 movie frames
dose rate: 153 e/p/s
total dose: 50 e/A2
dose per movie frame: 5 e/A2/frame

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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Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

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)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

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