EMD-2057
Cryo-EM structure of HBV T=4 empty Cp183 capsid
EMD-2057
Single-particle5.5 Å
Deposition: 21/03/2012
Map released: 03/04/2013
Last modified: 24/07/2013
Concentration: 0.24
mg/mL
Buffer
pH: 7.5
Details: 250 mM NaCl, 50 mM HEPES, 2 mM DTT
Details: 250 mM NaCl, 50 mM HEPES, 2 mM 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
Chamber humidity: 100%
Chamber temperature: 93 K
Instrument: FEI VITROBOT MARK III
Method: Blot for 4 seconds before plunging
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: 0.16 µm - 4.1 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: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 1.1 mm
Nominal defocus: 0.16 µm - 4.1 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: 594
Average electron dose per image: 14 e/Å2
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 594
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: 0.16 µm - 4.1 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: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 1.1 mm
Nominal defocus: 0.16 µm - 4.1 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: 594
Average electron dose per image: 14 e/Å2
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 594
Average electron dose per image: 14 e/Å2
Final
reconstruction
Resolution: 5.5
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 27489
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 27489
⌯ Applied Symmetry
Point group:
I
Software
[1]
Name | Version | Details |
---|---|---|
Auto3dem | - | - |
CTF correction
Details:Each particle phase-flipping
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of HBV T=4 empty Cp183 capsid
Details: ::::EMDATABANK.org::::EMD-2057::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of HBV T=4 empty Cp183 capsid
Details: ::::EMDATABANK.org::::EMD-2057::::
⬡ 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 | 0.6 | AUTHOR |