EMD-0333
Helical RNA-bound Hantaan virus nucleocapsid
EMD-0333
Helical reconstruction3.3 Å
Deposition: 01/11/2018Map released: 23/01/2019
Last modified: 15/05/2024
Concentration: 0.6
mg/mL
Buffer
pH: 8.0
Buffer components [5]:
Buffer components [5]:
| Name | Formula | Concentration | ChEBI |
|---|---|---|---|
| Tris-HCl | - | 20.0 mM | - |
| Sodium chloride | NaCl | 300.0 mM | |
| Magnesium chloride | MgCl2 | 10.0 mM | |
| Beta-mercapto-ethanol | - | 2.0 mM | - |
| Imidazole | - | 20.0 mM | - |
Grid
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 293 K
Instrument: FEI VITROBOT MARK IV
Details: 3 ul of sample were applied on the resulting glow-discharged grids and excess solution was blotted during 2.5 sec force 7.
Chamber humidity: 100%
Chamber temperature: 293 K
Instrument: FEI VITROBOT MARK IV
Details: 3 ul of sample were applied on the resulting glow-discharged grids and excess solution was blotted during 2.5 sec force 7.
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
Calibrated defocus: 0.8 µm - 3.5 µm
Calibrated magnification: 46860.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Calibrated defocus: 0.8 µm - 3.5 µm
Calibrated magnification: 46860.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Specialist optics
Energy filter
Name:
GIF Quantum LS
Image Recording
[1]
Detector model:
GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3840 pixel x 3712 pixel
Frames per image: 3-18
Number of grids: 1
Number of real images: 4328
Average electron dose per image: 40.0 e/Å2
Detector mode: COUNTING
Dimensions: 3840 pixel x 3712 pixel
Frames per image: 3-18
Number of grids: 1
Number of real images: 4328
Average electron dose per image: 40.0 e/Å2
Final
reconstruction
Resolution: 3.3
Å
(
BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 105665
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 105665
⌯ Applied Symmetry
Software
[1]
| Name | Version | Details |
|---|---|---|
| RELION | 3.0 | - |
Startup model
[1]
⦩ Final angle assignment
Type:
NOT APPLICABLE
Details: Relion was used for helical symmetry search/refinement on the best segments (removing the ones with more than 20 degree angular tilt) with local CTF determination and CTF-refinement. Frames 3-18 were used.
Details: Relion was used for helical symmetry search/refinement on the best segments (removing the ones with more than 20 degree angular tilt) with local CTF determination and CTF-refinement. Frames 3-18 were used.
Software
[1]
| Name | Version | Details |
|---|---|---|
| RELION | 2.1 | - |
Segment selection
[1]
| Number selected | Segment length | Segment overlap | Total filament length | Details |
|---|---|---|---|---|
| 168709 | - | - | - | Straight HTNV-NC were manually picked and computationally cut with an inter-box distance of 38 A along the helical axis into overlapping boxes of 400*400 pixels, resulting in 168,709 extracted segments. 2D classification was used to eliminate bad quality filaments. |
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Helical RNA-bound Hantaan virus nucleocapsid structure
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Helical RNA-bound Hantaan virus nucleocapsid structure
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Origin | 0 | 0 | 0 |
| Dimensions (px) | 400 | 400 | 400 |
| Dimensions (Å) | 426.80002 | 426.80002 | 426.80002 |
| Voxel size (Å) | 1.067 | 1.067 | 1.067 |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 0.025 | AUTHOR |