EMD-2060

Single-particle
7.0 Å
EMD-2060
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Deposition: 21/03/2012
Map released: 03/04/2013
Last modified: 24/07/2013
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EMD-2060
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EMICSS annotations (xml)

Cryo-EM structure of HBV T=4 empty Cp183 capsid

EMD-2060

Single-particle
7.0 Å
EMD-2060
3D View Gallery
Deposition: 21/03/2012
Map released: 03/04/2013
Last modified: 24/07/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.4
Details: 150mM NaCl, 50mM Tris, 2mM DTT
Grid
Details: Quantifoil R 2/2 holey carbon 200 mesh copper grids
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 93 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 4 seconds before plunging
Microscopy [2]
Microscope: JEOL 3200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 1.1 mm
Nominal defocus: 0.54 µm - 4.87 µm
Nominal magnification: 80000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification, Electron beam tilt params: )
Temperature
Average: 97 K
Specialist optics
Energy filter
Name: Omega filter
Image Recording [1]
Detector category: CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 394
Average electron dose per image: 14 e/Å2
Microscope: JEOL 3200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 1.1 mm
Nominal defocus: 0.54 µm - 4.87 µm
Nominal magnification: 80000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification, Electron beam tilt params: )
Temperature
Average: 97 K
Specialist optics
Energy filter
Name: Omega filter
Image Recording [1]
Detector category: CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 394
Average electron dose per image: 14 e/Å2
Image processing [1]
Final reconstruction
Resolution: 7.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 7439
⌯ Applied Symmetry
Point group: I
Software [1]
Name Version Details
Auto3dem - -
CTF correction
Details:Each particle phase-flipping
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM structure of HBV T=4 pgRNA-filled Cp183 capsid at phosphorylation-mimic state (Cp183RNA-EEE)
Details: ::::EMDATABANK.org::::EMD-2060::::
⬡ Geometry
X Y Z
Dimensions 301 301 301
Origin -150 -150 -150
Spacing 301 301 301
Voxel size 1.4836 Å 1.4836 Å 1.4836 Å
Contour list
Primary Level Source
True 35.0 AUTHOR