EMPIAR-13549 - Experimentally-grounded benchmark datasets for cryoEM heterogeneous reconstruction methods with engineered Cas9 complexes [multiple data sets in EER and MRCS formats]

EMPIAR-13549

Experimentally-grounded benchmark datasets for cryoEM heterogeneous reconstruction methods with engineered Cas9 complexes [multiple data sets in EER and MRCS formats]

Publication:

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

Grassetti AV, Kinman LF, Davis JH

(---)

DOI: 10.64898/2026.05.04.721978

Related EMDB entry:

EMD-76398 EMD-76392 EMD-76405 EMD-76407 EMD-76396 EMD-76401 EMD-76406 EMD-76400 EMD-76391 EMD-76402

Deposited:

2026-03-11

Released:

2026-09-11

Last modified:

2026-09-11

Imageset size:

33.20 TB

Imageset DOI:

10.6019/EMPIAR-13549

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

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

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

7100

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

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:

EER

No. of images or tilt series:

4563

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 3 bp extension.

Files:

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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:

EER

No. of images or tilt series:

5836

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 4 bp extension.

Files:

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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:

EER

No. of images or tilt series:

4682

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 5 bp extension.

Files:

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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:

EER

No. of images or tilt series:

6073

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 6 bp extension.

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:

EER

No. of images or tilt series:

5357

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 7 bp extension.

Files:

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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:

EER

No. of images or tilt series:

5137

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 8 bp extension.

Files:

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8. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 9 bp extension

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5308

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 9 bp extension.

Files:

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9. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 10 bp extension

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

6048

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 10 bp extension.

Files:

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10. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 11 bp extension

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5019

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 11 bp extension.

Files:

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11. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 12 bp extension

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

4949

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 12 bp extension.

Files:

This entry cannot be downloaded from PDBj.

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12. Unaligned multiframe micrographs of dCas9 in complex with sgRNA and target DNA bearing 13 bp extension

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5474

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

Details:

Raw, unaligned movies of dCas9 complexes with 13 bp extension.

Files:

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

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5507

Image size:

(4096, 4096)

Pixel type:

BIT

Pixel spacing:

(0.641, 0.641)

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.

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14. Jointly-polished particles with DNA extension lengths from 2-14 bp

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

2904834

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.12175, 1.12175)

Details:

Filtered particles from all 13 datasets, refined and jointly-polished. Other job189*.star files reference curated or subsampled subsets (see particle_stacks/README.md).

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15. Jointly-polished particles with 2 bp, 8 bp, and 14 bp DNA extension lengths

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

811374

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.641, 0.641)

Details:

Filtered particles from 2 bp, 8 bp, and 14 bp datasets, refined and jointly-polished. Other job149*.star files reference curated or subsampled subsets (see particle_stacks/README.md).

Files:

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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)

Helical reconstruction of amyloids in cryoSPARC.

Schaefer JH, O'Neill RT, Donnelly JP, Powers ET, Kelly JW, Lander GC. (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)

An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.

Marchán Torres D, Conesa P, Garcia A, Iceta M, Broche L, Gragera M, Linares R, Kwong HS, Chichón FJ, Svensson O, Arranz R, Effantin G, Kandiah E, Carazo JM, Sorzano COS. (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.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Unbend, correction of local beam-induced sample motion in cryo-EM images using a 3D spline model.

Kong L, Zottig X, Elferich J, Grigorieff N. (2026)

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)

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

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

See all citations

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