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- EMDB-0442: Type III-A CRISPR Effector Subcomplex from Staphylococcus epiderm... -

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Basic information

Entry
Database: EMDB / ID: 0442
TitleType III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a
Map dataType III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a, primary map
SampleType III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a:
SourceStaphylococcus epidermidis RP62A (bacteria)
Methodsingle particle reconstruction / cryo EM / 5.2 Å resolution
AuthorsDorsey BW / Mondragon A
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM.
Authors: Bryan W Dorsey / Lei Huang / Alfonso Mondragón
DateDeposition: Dec 13, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Feb 13, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0442.map.gz (map file in CCP4 format, 58108 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
244 pix
1.24 Å/pix.
= 302.56 Å
244 pix
1.24 Å/pix.
= 302.56 Å
244 pix
1.24 Å/pix.
= 302.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density
Contour Level:0.0185 (by author), 0.01 (movie #1):
Minimum - Maximum-0.027626785 - 0.0711628
Average (Standard dev.)0.00000088811134 (0.0019536428)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions244244244
Origin0.00.00.0
Limit243.0243.0243.0
Spacing244244244
CellA=B=C: 302.56 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z244244244
origin x/y/z0.0000.0000.000
length x/y/z302.560302.560302.560
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS244244244
D min/max/mean-0.0280.0710.000

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Supplemental data

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Sample components

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Entire Type III-A CRISPR Effector Subcomplex from Staphylococcus epiderm...

EntireName: Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a
Number of components: 1

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Component #1: protein, Type III-A CRISPR Effector Subcomplex from Staphylococcu...

ProteinName: Type III-A CRISPR Effector Subcomplex from Staphylococcus epidermidis RP62a
Recombinant expression: No
MassExperimental: 255 kDa
SourceSpecies: Staphylococcus epidermidis RP62A (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 8
Support filmGlow discharged with 15mA.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 99 %
Details: Blot for 4 seconds with +5 force before plunging..

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 37.5 e/Å2 / Illumination mode: OTHER
LensMagnification: 30000.0 X (nominal), 40323.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 3500.0 nm / Energy filter: In-column Omega Filter
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 100.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1037 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 107620
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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