EMD-9055

Single-particle
3.46 Å
EMD-9055
3D View Gallery
Deposition: 27/08/2018
Map released: 19/12/2018
Last modified: 09/01/2019
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-9055
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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 6mzi summary report (pdf.gz) Map and 6mzi FULL report (pdf.gz)
EMICSS annotations (xml)

CryoEM structure of human enterovirus D68 expanded 1 particle (pH 6.5, 4 degrees Celsius, 3 min)

EMD-9055

Single-particle
3.46 Å
EMD-9055
3D View Gallery
Deposition: 27/08/2018
Map released: 19/12/2018
Last modified: 09/01/2019
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 6.5
Details: Phosphate citrate buffer
Grid
Mesh: 400
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Pressure: 0.02 kPa
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 80%
Chamber temperature: 298 K
Instrument: GATAN CRYOPLUNGE 3
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: 100.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.5 µm - 8.5 µm
Nominal magnification: 81000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Specialist optics
Energy filter
Name: GIF Quantum LS
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Sampling interval: 5.0 µm
Number of grids: 1
Number of real images: 357
Average exposure time: 10.5 s
Average electron dose per image: 28.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.46 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 4968
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: I
Software [1]
Name Version Details
Jspr - -
Startup model [1]
Type: OTHER
Details:Particle orientations were randomly assigned.
⦨ Initial angle assignment
Type: RANDOM ASSIGNMENT
Software [1]
Name Version Details
Jspr - -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Angular sampling: 0.5 degrees
Software [1]
Name Version Details
Jspr - -
Particle selection [1]
Selected Ref. model Method Software Details
39022 - - - -
Final 3D classification
Details: 33863 particles were selected after 2D classification. Subsequently, 3D classification yielded full native virions, A-particles and expanded 1 particles.
Software [1]
Name Version Details
RELION 2.1.0 -
CTF correction
Details: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Software [1]
Name Version Details
Jspr - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Sharpened map in which the inner density is masked out
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 264 264 264
Dimensions (Å) 456.72 456.72 456.72
Voxel size (Å) 1.73 1.73 1.73
Contour list
Primary Level Source
True 18.7 AUTHOR