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- EMDB-7346: CRISPR RNA-guided surveillance complex, post-nicking -

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Basic information

Entry
Database: EMDB / ID: EMD-7346
TitleCRISPR RNA-guided surveillance complex, post-nicking
Map dataCryo-EM map of Type 1-E Cascade-Cas3 complex at the state of post-NTS-nicking
Sample
  • Complex: CRISPR RNA-guided surveillance complex with Cas3 bound in its post-nicking state
Biological speciesThermobifida fusca (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsXiao Y / Luo M
CitationJournal: To Be Published
Title: CRISPR RNA-guided surveillance complex, post-nicking
Authors: Xiao Y / Luo M / Liao M / Ke A
History
DepositionJan 17, 2018-
Header (metadata) releaseFeb 7, 2018-
Map releaseJan 23, 2019-
UpdateJan 23, 2019-
Current statusJan 23, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7346.png

Downloads & links

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Map

FileDownload / File: emd_7346.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Type 1-E Cascade-Cas3 complex at the state of post-NTS-nicking
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.05889012 - 0.10720145
Average (Standard dev.)-0.000010154122 (±0.0059975735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0590.107-0.000

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Supplemental data

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Sample components

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Entire : CRISPR RNA-guided surveillance complex with Cas3 bound in its pos...

EntireName: CRISPR RNA-guided surveillance complex with Cas3 bound in its post-nicking state
Components
  • Complex: CRISPR RNA-guided surveillance complex with Cas3 bound in its post-nicking state

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Supramolecule #1: CRISPR RNA-guided surveillance complex with Cas3 bound in its pos...

SupramoleculeName: CRISPR RNA-guided surveillance complex with Cas3 bound in its post-nicking state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Thermobifida fusca (bacteria) / Strain: YX
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pcdf

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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

Concentration1.0 mg/mL
BufferpH: 7.5 / Details: 10 mM Hepes, 150 mM NaCl, 5 mM DTT, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 %

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80.0 K / Max: 105.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1428 / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.7 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 322268
CTF correctionSoftware - Name: RELION (ver. 1.4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 10820
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SAMUEL
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)

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Atomic model buiding 1

RefinementSpace: REAL

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