EMD-5536

Subtomogram averaging
40.0 Å
EMD-5536
3D View Gallery
Deposition: 04/12/2012
Map released: 04/09/2013
Last modified: 25/09/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5536
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EMICSS annotations (xml)

Visualization of Bacteriophage T7 Infection by Cryo-Electron Tomography

EMD-5536

Subtomogram averaging
40.0 Å
EMD-5536
3D View Gallery
Deposition: 04/12/2012
Map released: 04/09/2013
Last modified: 25/09/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.8
Details: 50 mM Tris-HCl, 10 mM MgCl2, 0.1 M NaCl
Grid
Details: 200 mesh grid
Vitrification
Cryogen name: ETHANE
Chamber temperature: 100 K
Instrument: HOMEMADE PLUNGER
Method: Blot for 3 seconds before plunging.
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal defocus: 4.0 µm - 6.0 µm
Nominal magnification: 31000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Liquid Nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 200,000x magnification, Electron beam tilt params: )
Temperature
Minimum: 90 K
Average: 95 K
Maximum: 100 K
Image Recording [1]
Detector category: CCD
Detector model: GENERIC TVIPS (4k x 4k)
Average electron dose per image: 100 e/Å2
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-64 ° 64 ° - - - - -
Image processing [1]
Details: The particles were manually selected from cryo-tomograms.
Final reconstruction
Resolution: 40.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
IMOD, Raptor, Protomo - -
Final 3D classification
Number of classes: 4
CTF correction
Details:No CTF correction
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Asymmetric reconstruction of bacteriophage fiberless virion
Details: ::::EMDATABANK.org::::EMD-5536::::
⬡ Geometry
X Y Z
Dimensions 140 140 180
Origin -70 -70 -90
Spacing 140 140 180
Voxel size 5.7 Å 5.7 Å 5.7 Å
Contour list
Primary Level Source
True 1.0 AUTHOR