EMD-0290

Subtomogram averaging
7.2 Å
EMD-0290
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Deposition: 12/10/2018
Map released: 05/12/2018
Last modified: 19/12/2018
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-0290
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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 6hwi summary report (pdf.gz) Map and 6hwi FULL report (pdf.gz)
EMICSS annotations (xml)

Immature M-PMV capsid hexamer structure in intact virus particles

EMD-0290

Subtomogram averaging
7.2 Å
EMD-0290
3D View Gallery
Deposition: 12/10/2018
Map released: 05/12/2018
Last modified: 19/12/2018
Overview 3D View Sample Experiment Validation Volume Browser 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
Sampling interval: 5.0 µm
Frames per image: 1-6
Number of grids: 1
Average exposure time: 0.6 s
Average electron dose per image: 2.0 e/Å2
Details: Dose fluctuation was caused by the ring collapse of FEG during data collection.
Image processing [1]
Final reconstruction
Resolution: 7.2 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
⌯ 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: 17109
Software [2]
Name Version Details
AmiraFPM - Volume selection
MATLAB - Volume extraction
CTF correction
Software [2]
Name Version Details
MATLAB - CTF determination
IMOD - Phase flipping only
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: None
⬡ Geometry
X Y Z
Dimensions 192 192 192
Origin 0 0 0
Spacing 192 192 192
Voxel size 1.35 Å 1.35 Å 1.35 Å
Contour list
Primary Level Source
True 0.118 AUTHOR