EMPIAR-10588 - Cryo-EM reconstruction of heavy chain mouse apoferritin, 8 datasets testing dose rate and correlative double sampling mode for the Gatan K3 direct electron detector. [1143 multi-frame micrographs composed of 120 frames in LZW compressed TIFF format [multiple data sets in TIFF format]

EMPIAR-10588

Cryo-EM reconstruction of heavy chain mouse apoferritin, 8 datasets testing dose rate and correlative double sampling mode for the Gatan K3 direct electron detector. [1143 multi-frame micrographs composed of 120 frames in LZW compressed TIFF format [multiple data sets in TIFF format]

Publication:

Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM

Sun M, Azumaya CM, Tse E, Bulkley DP, Harrington MB, Gilbert G, Frost A, Southworth D, Verba KA, Cheng Y, Agard DA

Journal of structural biology 213 (2021)

PMID: 33984504

DOI: 10.1016/j.jsb.2021.107745

Related EMDB entry:

EMD-22972

Deposited:

2020-11-10

Released:

2021-11-26

Last modified:

2021-11-26

Imageset size:

8.48 TB

Imageset DOI:

10.6019/EMPIAR-10588

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 8 e/p/s in CDS mode from Gatan K3

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1143

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.417, 0.417)

Details:

1143 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 8 e-/pix/s dose rate dataset at 105kx nominal magnification collected in CDS mode of Gatan K3.

Files:

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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)

2. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 8 e/p/s in standard mode from Gatan K3

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1143

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.417, 0.417)

Details:

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. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 4 e/p/s in CDS mode from Gatan K3

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1143

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.417, 0.417)

Details:

1143 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 4 e-/pix/s dose rate dataset at 105kx nominal magnification collected in CDS mode of Gatan K3.

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. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 4 e/p/s in CDS mode from Gatan K3

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1152

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.417, 0.417)

Details:

1152 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 16 e-/pix/s dose rate dataset at 105kx nominal magnification collected in CDS mode of Gatan K3.

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. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 8 e/p/s in CDS mode from Gatan K3 at lower magnification

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1080

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.673, 0.673)

Details:

1080 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 8 e-/pix/s dose rate dataset at 64kx nominal magnification collected in CDS mode of Gatan K3.

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. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 8 e/p/s in standard mode from Gatan K3 at lower magnification

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1107

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.673, 0.673)

Details:

1107 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 8 e-/pix/s dose rate dataset at 64kx nominal magnification collected in standard mode of Gatan K3.

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)

7. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 16 e/p/s in CDS mode from Gatan K3 at lower magnification

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1152

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.673, 0.673)

Details:

1152 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 16 e-/pix/s dose rate dataset at 64kx nominal magnification collected in CDS mode of Gatan K3.

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)

8. apoferritin multi-frame raw micrographs non gain normalized frames in LZW compressed TIFF format collected at 16 e/p/s in standard mode from Gatan K3 at lower magnification

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1143

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.673, 0.673)

Details:

1143 multi-frame raw micrographs composed of 120 frames each in LZW compressed TIFF format, along with separate gain reference for the 16 e-/pix/s dose rate dataset at 64kx nominal magnification collected in standard mode of Gatan K3.

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)

Browse All Files

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)

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

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)

See all citations

Protein Data Bank Japan News

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

294 new PDB entries have been released on 2024-10-30.

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024

[2024-10-16]

[wwPDB] wwPDB Data Release Policy on Public Preprint Archives