EMD-5410
Cryo-electron microscopic reconstruction of wild rabbit hemorrhagic disease virus
EMD-5410
Single-particle6.5 Å
Deposition: 07/04/2012Map released: 30/01/2013
Last modified: 06/02/2013
Buffer
pH: 7.0
Details: 50mM Tris, 50mM NaCl, 5mM EDTA
Details: 50mM Tris, 50mM NaCl, 5mM EDTA
Grid
Details: 200 mesh copper grid with holey array carbon support (GiG), glow discharged
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 100 K
Instrument: FEI VITROBOT MARK IV
Method: Blot for 3 seconds before plunging
Chamber humidity: 100%
Chamber temperature: 100 K
Instrument: FEI VITROBOT MARK IV
Method: Blot for 3 seconds before plunging
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.5 µm - 2.5 µm
Nominal magnification: 96000.0
Calibrated magnification: 160770.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Specimen holder details: Liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: 0)
Minimum tilt angle: 0
Maximum tilt angle: 0
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.5 µm - 2.5 µm
Nominal magnification: 96000.0
Calibrated magnification: 160770.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Specimen holder details: Liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: 0)
Minimum tilt angle: 0
Maximum tilt angle: 0
Temperature
Average: 85
K
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Number of real images: 1100
Average electron dose per image: 20 e/Å2
Bits per pixel: 32.0
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Number of real images: 1100
Average electron dose per image: 20 e/Å2
Bits per pixel: 32.0
Details: The particles were selected using an automatic selection program FindEM.
Final
reconstruction
Resolution: 6.5
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 26000
Algorithm: OTHER
Details: The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom.
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 26000
Algorithm: OTHER
Details: The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom.
⌯ Applied Symmetry
Point group:
I
Software
[1]
| Name | Version | Details |
|---|---|---|
| EMAN1.9, Spider | - | - |
Final 2D classification
Number of classes:
475
CTF correction
Details:CTF correction of each whole micrograph
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of wild rabbit hemorrhagic disease virus; The final map was sharpened using b factor -300 A2 to 4.5 angstrom and low passed to 5 angstrom.
Details: ::::EMDATABANK.org::::EMD-5410::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of wild rabbit hemorrhagic disease virus; The final map was sharpened using b factor -300 A2 to 4.5 angstrom and low passed to 5 angstrom.
Details: ::::EMDATABANK.org::::EMD-5410::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 480 | 480 | 480 |
| Origin | -240 | -240 | -240 |
| Spacing | 480 | 480 | 480 |
| Voxel size | 0.933 Å | 0.933 Å | 0.933 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 2.6 | AUTHOR |