EMD-5743

Subtomogram averaging
74.0 Å
EMD-5743
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Deposition: 13/08/2013
Map released: 09/10/2013
Last modified: 06/11/2013
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EMD-5743
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Zernike Phase Contrast electron cryo-tomography of cyanophage Syn5 assembly intermediates

EMD-5743

Subtomogram averaging
74.0 Å
EMD-5743
3D View Gallery
Deposition: 13/08/2013
Map released: 09/10/2013
Last modified: 06/11/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 8.0
Details: Artificial sea water
Grid
Details: 200 mesh Quantifoil holey grids, glow discharged
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 85 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 3 seconds before plunging
Microscopy [1]
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 4.1 mm
Nominal defocus: 0.0 µm - 1.0 µm
Nominal magnification: 25000.0
Calibrated magnification: 25000.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: )
Temperature
Minimum: 93 K
Average: 103 K
Maximum: 105 K
Specialist optics
Energy filter
Name: In-column GIF energy filter
Lower energy threshold: 15.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 42
Average electron dose per image: 1 e/Å2
Detector distance: 1200
Bits per pixel: 16.0
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-60 ° 60 ° - - - - -
Image processing [1]
Details: The subtomograms were extracted from infected cells.
Final reconstruction
Resolution: 74.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
IMOD - -
Final 3D classification
Number of classes: 1
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cyanophage Syn5 assembly intermediate - the expanded capsid
Details: ::::EMDATABANK.org::::EMD-5743::::
⬡ Geometry
X Y Z
Dimensions 128 128 128
Origin 32 32 32
Spacing 128 128 128
Voxel size 9.04 Å 9.04 Å 9.04 Å
Contour list
Primary Level Source
True 1.9 AUTHOR