EMPIAR-10437 - Single-particle cryo-EM of the full-length merozoite surface protein 1 from Plasmodium falciparum [multiple data sets in MRC and MRCS formats]

EMPIAR-10437

Single-particle cryo-EM of the full-length merozoite surface protein 1 from Plasmodium falciparum [multiple data sets in MRC and MRCS formats]

Publication:

Structure of the merozoite surface protein 1 from Plasmodium falciparum

Dijkman PM, Marzluf T, Zhang Y, Chang SYS, Helm D, Lanzer M, Bujard H, Kudryashev M

Science advances 7 (2021)

PMID: 34078606

DOI: 10.1126/sciadv.abg0465

Related EMDB entry:

EMD-11151 EMD-11154 EMD-11152 EMD-11153 EMD-11157 EMD-11150 EMD-11155 EMD-11156

Deposited:

2020-06-08

Released:

2021-11-08

Last modified:

2021-11-08

Imageset size:

4.33 TB

Imageset DOI:

10.6019/EMPIAR-10437

Experimental metadata:

Download xml json

Compressed by PDBj:

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

Movies in the micrographs directory of this entry were compressed to TIFF by EMPIAR Japan to save space and bandwidth.
The compression is lossless in that all pixel intensities remain exactly the same after decompression.
However, some metadata in the MRC header were lost.
The original files before compression are available from EMPIAR EBI.

Compression was carried out by separating (“un-normalizing”) the gain.
The details of the method are described in
https://relion.readthedocs.io/en/release-3.1/Reference/MovieCompression.html#gain-normalised-movies.

Please apply the gain reference (e.g. hdMSP1/gain-reference.mrc) in the respective folder during processing.
Note that the movies in hdMSP1-dataset3 were grouped into three sets, which differ by the gain.

Original size:   36,122,534,732 kilobytes
Compressed size:  4,282,869,455 kilobytes

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned movies of MSP-1

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

3734

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Unaligned, gain-corrected, 40-frame movies, recorded automatically with EPU, using K2 camera in counting mode on a Titan Krios microscope operated at 300 kV at a nominal magnification of 130 000, corresponding to a pixel size of 1.073 Å. The total electron dose per micrograph: ~64 e-/Å^2.

Files:

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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.

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

2. Unaligned movies of hdMSP-1 (dataset 1)

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

1685

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.077, 1.077)

Details:

Unaligned, gain-corrected, 40-frame movies, recorded automatically with EPU, using K2 camera in counting mode on a Titan Krios microscope operated at 300 kV at a nominal magnification of 130 000, corresponding to a pixel size of 1.077 Å. The total electron dose per micrograph: ~60 e-/Å^2.
Datasets 1-4 were combined for reconstruction of hdMSP-1.

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. Unaligned movies of hdMSP-1 (dataset 2)

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

3560

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.077, 1.077)

Details:

Unaligned, gain-corrected, 40-frame movies, recorded automatically with EPU, using K2 camera in counting mode on a Titan Krios microscope operated at 300 kV at a nominal magnification of 130 000, corresponding to a pixel size of 1.077 Å. The total electron dose per micrograph: ~60 e-/Å^2.
Datasets 1-4 were combined for reconstruction of hdMSP-1.

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. Unaligned movies of hdMSP-1 (dataset 3)

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

5864

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.077, 1.077)

Details:

Unaligned, gain-corrected, 40-frame movies, recorded automatically with EPU, using K2 camera in counting mode on a Titan Krios microscope operated at 300 kV at a nominal magnification of 130 000, corresponding to a pixel size of 1.077 Å. The total electron dose per micrograph: ~60 e-/Å^2.
Datasets 1-4 were combined for reconstruction of hdMSP-1.

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. Unaligned movies of hdMSP-1 (dataset 4)

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

1393

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.077, 1.077)

Details:

Unaligned, gain-corrected, 40-frame movies, recorded automatically with EPU, using K2 camera in counting mode on a Titan Krios microscope operated at 300 kV at a nominal magnification of 130 000, corresponding to a pixel size of 1.077 Å. The total electron dose per micrograph: ~60 e-/Å^2.
Datasets 1-4 were combined for reconstruction of hdMSP-1. Dataset 4 was collected at 15 degrees tilt.

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. Final particle stack for hdMSP-1 conformation 1

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

271763

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.077, 1.077)

Details:

Final 271,763 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for hdMSP-1 (conformation 1); box size 288 pixels, 1.077 Å/pixel.

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. Final particle stack for hdMSP-1 conformation 2

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

182515

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.077, 1.077)

Details:

Final 182,515 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for hdMSP-1 (conformation 2); box size 288 pixels, 1.077 Å/pixel.

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. Final particle stack for MSP-1 main conformation

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

141838

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Final 141,838 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for MSP-1 (main conformation); box size 288 pixels, 1.073 Å/pixel.

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)

9. Final particle stack for MSP-1 alternative conformation 1

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

112939

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Final 112,939 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for MSP-1 (alternative conformation 1); box size 288 pixels, 1.073 Å/pixel.

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)

10. Final particle stack for MSP-1 alternative conformation 2

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

118878

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Final 118,878 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for MSP-1 (alternative conformation 2); box size 288 pixels, 1.073 Å/pixel.

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)

11. Final particle stack for MSP-1 alternative conformation 3

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

124774

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Final 124,774 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for MSP-1 (alternative conformation 3); box size 288 pixels, 1.073 Å/pixel.

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)

12. Final particle stack for MSP-1 alternative conformation 4

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

116037

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Final 116,037 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for MSP-1 (alternative conformation 4); box size 288 pixels, 1.073 Å/pixel.

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)

13. Final particle stack for MSP-1 alternative conformation 5

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

75620

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.073, 1.073)

Details:

Final 75,620 particle stack and corresponding starfile (converted from cryoSPARC particle file using USCF pyem) for MSP-1 (alternative conformation 5); box size 288 pixels, 1.073 Å/pixel.

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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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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