EMD-17947

Single-particle
4.0 Å
EMD-17947
3D View Gallery
Deposition: 17/07/2023
Map released: 17/07/2024
Last modified: 23/10/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-17947
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

Trimeric prM/E spike of Tick-borne encephalitis virus immature particle

EMD-17947

Single-particle
4.0 Å
EMD-17947
3D View Gallery
Deposition: 17/07/2023
Map released: 17/07/2024
Last modified: 23/10/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 2 mg/mL
Details: Purified immature particles of Tick-borne encephalitis virus
Buffer
pH: 8.5
Buffer components [3]:
Name Formula Concentration ChEBI
Trizma Tris 20.0 mM
Sodium Chloride NaCl 120.0 mM
- EDTA 1.0 mM
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 280 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 30.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 1.0 µm - 3.0 µm
Nominal magnification: 105000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Detector mode: INTEGRATING
Number of grids: 1
Number of real images: 11246
Average exposure time: 2.0 s
Average electron dose per image: 40.0 e/Å2
Details: Collected in movie mode total 40 fractions per micrograph
Image processing [1]
Final reconstruction
Resolution: 4.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 552993
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 3.1 -
Startup model [1]
Type: OTHER
Details:Backprojection from localized recon subparticle extraction
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.1 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.1 -
Particle selection [1]
Selected Ref. model Method Software Details
1639578 - - - Picked as sub-particles form original whole immature particle reconstruction
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Tick-borne encephalitis virus (strain Neudoerfl) immature particle E/prM spike trimer main map
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 300 300 300
Dimensions (Å) 250.08 250.08 250.08
Voxel size (Å) 0.8336 0.8336 0.8336
Contour list
Primary Level Source
True 0.008 AUTHOR