EMD-0291

Subtomogram averaging
6.6 Å
EMD-0291
3D View Gallery
Deposition: 15/10/2018
Map released: 05/12/2018
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-0291
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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)
Map and PDB model 6hww summary report (pdf.gz) Map and 6hww FULL report (pdf.gz)
EMICSS annotations (xml)

Immature MLV capsid hexamer structure in intact virus particles

EMD-0291

Subtomogram averaging
6.6 Å
EMD-0291
3D View Gallery
Deposition: 15/10/2018
Map released: 05/12/2018
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Details: Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold.
Buffer
pH: 6.0
Grid
Mesh: 300
Model: C-flat-2/1
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 288 K
Instrument: FEI VITROBOT MARK II
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: 50.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 2.0 µm - 4.5 µm
Nominal magnification: 105000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: ZEMLIN TABLEAU
Specialist optics
Energy filter
Name: GIF Quantum LS
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 QUANTUM (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 1-6
Number of grids: 1
Average exposure time: 0.6 s
Average electron dose per image: 2.5 e/Å2
Image processing [1]
Final reconstruction
Resolution: 6.6 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C6
Software [2]
Name Version Details
AV3 - -
TOM - -
⦩ Final angle assignment
Type: OTHER
Details: Subtomogram Averaging.
Software [2]
Name Version Details
AV3 - -
TOM - -
Extraction
Number of images used: 23141
Software [2]
Name Version Details
AmiraFPM - Volume selection
MATLAB - Volume extraction
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: None
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 192 192 192
Dimensions (Å) 259.2 259.2 259.2
Voxel size (Å) 1.35 1.35 1.35
Contour list
Primary Level Source
True 0.125 AUTHOR