EMD-0298

Helical reconstruction
4.1 Å
EMD-0298
3D View Gallery
Deposition: 18/10/2018
Map released: 07/08/2019
Last modified: 07/08/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-0298
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 6hxz summary report (pdf.gz) Map and 6hxz FULL report (pdf.gz)
EMICSS annotations (xml)

Virus-like Particles based on Potato Virus Y

EMD-0298

Helical reconstruction
4.1 Å
EMD-0298
3D View Gallery
Deposition: 18/10/2018
Map released: 07/08/2019
Last modified: 07/08/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Helical reconstruction
Aggregation State: Filament
Specimen preparation [1]
Concentration: 6.7 mg/mL
Buffer
pH: 7.4
Buffer components [1]:
Name Formula Concentration ChEBI
Phosphate buffered saline PBS 12.0 mM
Details: 140 mM NaCl 2.7 mM KCl
Grid
Model: Quantifoil R2/1
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Vitrification
Cryogen name: ETHANE
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: OTHER
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 1.0 µm - 2.2 µm
Nominal magnification: 75000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: ZEMLIN TABLEAU
Image Recording [1]
Detector model: FEI FALCON II (4k x 4k)
Detector mode: INTEGRATING
Dimensions: 4096 pixel x 4096 pixel
Frames per image: 1-16
Number of real images: 5344
Average electron dose per image: 48.6 e/Å2
Image processing [1]
Final reconstruction
Resolution: 4.1 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 148876
⌯ Applied Symmetry
ΔΖ: 42.65 Å
ΔΦ: 13.24°
Axial symmetry: C8
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: Featureless cylinder constructed in Relion.
⦩ Final angle assignment
Type: NOT APPLICABLE
CTF correction
Software [1]
Name Version Details
Gctf 1.05 -
Segment selection [1]
Number selected Segment length Segment overlap Total filament length Details
244988 - - - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: CryoEM map of Virus-Like Particle from Potato virus Y
⬡ Geometry
X Y Z
Dimensions 360 360 360
Origin 0 0 0
Spacing 360 360 360
Voxel size 1.061 Å 1.061 Å 1.061 Å
Contour list
Primary Level Source
True 1.25 AUTHOR