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- EMDB-35374: Cas005-crRNA-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35374
TitleCas005-crRNA-DNA complex
Map data
Sample
  • Complex: Cas005 ternary complex with crRNA and target DNA
KeywordsCRISPR/cas005 / DNA-RNA HYBRID
Biological speciesphage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang X / Duan ZQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cas005-crRNA-DNA complex
Authors: Zhang X / Duan ZQ
History
DepositionFeb 14, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35374.png

Downloads & links

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Map

FileDownload / File: emd_35374.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.036287654 - 1.9078348
Average (Standard dev.)0.0007578411 (±0.017632436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35374_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35374_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35374_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cas005 ternary complex with crRNA and target DNA

EntireName: Cas005 ternary complex with crRNA and target DNA
Components
  • Complex: Cas005 ternary complex with crRNA and target DNA

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Supramolecule #1: Cas005 ternary complex with crRNA and target DNA

SupramoleculeName: Cas005 ternary complex with crRNA and target DNA / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: phage (virus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59179
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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