EMPIAR-13602 - Experimentally-grounded benchmark datasets for cryoEM heterogeneous reconstruction methods with engineered Cas9 complexes, alternate microscope collection [multiple data sets in TIFF format]

EMPIAR-13602

Experimentally-grounded benchmark datasets for cryoEM heterogeneous reconstruction methods with engineered Cas9 complexes, alternate microscope collection [multiple data sets in TIFF format]

Publication:

Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods

Grassetti AV, Kinman LF, Davis JH

bioRxiv (2026)

DOI: 10.64898/2026.05.04.721978

Related EMDB entry:

Deposited:

2026-05-05

Released:

2026-08-26

Last modified:

2026-08-26

Imageset size:

7.21 TB

Imageset DOI:

10.6019/EMPIAR-13602

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 2 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5458

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 2 bp extension

Files:

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2. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 3 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5343

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 3 bp extension

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.

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3. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 4 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5504

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 4 bp extension

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.

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4. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 5 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

6567

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 5 bp extension

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.

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5. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 6 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5505

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 6 bp extension

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.

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6. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 7 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5354

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 7 bp extension

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.

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7. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 8 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5040

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 8 bp extension

Files:

This entry cannot be downloaded from PDBj.

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

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8. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 14 bp extension

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

5081

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.654, 0.654)

Details:

Raw, unaligned movies of dCas9 complexes with 14 bp extension

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.

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

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Citations

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM.

Ramírez-Aportela E, Zarrabeitia OL, Fonseca YC, Ceska T, Subramaniam S, Carazo JM, Sorzano COS. (2026)

A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.

Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (2026)

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

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CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

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Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (2026)

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