EMD-5563
Electron microscopy of Everglades virus
EMD-5563
Single-particle10.0 Å
Deposition: 06/01/2013Map released: 13/02/2013
Last modified: 27/02/2013
Concentration: 1
mg/mL
Buffer
pH: 7.4
Details: 0.05 M Tris HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA
Details: 0.05 M Tris HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA
Grid
Details: C-flat 1.2/1.3 holey film
Vitrification
Cryogen name: ETHANE
Chamber humidity: 60%
Chamber temperature: 90 K
Instrument: HOMEMADE PLUNGER
Method: blot for 4 seconds before plunging
Chamber humidity: 60%
Chamber temperature: 90 K
Instrument: HOMEMADE PLUNGER
Method: blot for 4 seconds before plunging
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.3 µm - 2.3 µm
Nominal magnification: 60000.0
Calibrated magnification: 74800.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626 70 degree holder
Alignment procedure: LEGACY (Astigmatism: manual correction at 150,000x, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.3 µm - 2.3 µm
Nominal magnification: 60000.0
Calibrated magnification: 74800.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626 70 degree holder
Alignment procedure: LEGACY (Astigmatism: manual correction at 150,000x, Electron beam tilt params: )
Temperature
Minimum: 87
K
Average: 88 K
Maximum: 90 K
Average: 88 K
Maximum: 90 K
Specialist optics
Energy filter
Name:
Omega
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Number of real images: 80
Average electron dose per image: 20 e/Å2
Bits per pixel: 16.0
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Number of real images: 80
Average electron dose per image: 20 e/Å2
Bits per pixel: 16.0
Details: Particles picked with EMAN2 boxer, reconstructed using IMAGIC-5
Final
reconstruction
Resolution: 10.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 1000
Algorithm: OTHER
Details: Final maps were calculated from individual particles
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 1000
Algorithm: OTHER
Details: Final maps were calculated from individual particles
⌯ Applied Symmetry
Point group:
I
Software
[1]
| Name | Version | Details |
|---|---|---|
| IMAGIC-5 | - | - |
⦩ Final angle assignment
Details: Icosahedral asymmetric unit
CTF correction
Details:Micrograph
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of wild type everglades virus
Details: ::::EMDATABANK.org::::EMD-5563::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of wild type everglades virus
Details: ::::EMDATABANK.org::::EMD-5563::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 200 | 200 | 200 |
| Origin | -100 | -100 | -100 |
| Spacing | 200 | 200 | 200 |
| Voxel size | 4 Å | 4 Å | 4 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 13.0 | EMDB |