EMD-8900

Single-particle
29.4 Å
EMD-8900
3D View Gallery
Deposition: 21/08/2017
Map released: 06/09/2017
Last modified: 29/01/2020
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-8900
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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)
EMICSS annotations (xml)

Negative stain reconstruction of human autophagy associated protein, ATG2A

EMD-8900

Single-particle
29.4 Å
EMD-8900
3D View Gallery
Deposition: 21/08/2017
Map released: 06/09/2017
Last modified: 29/01/2020
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.01 mg/mL
Buffer
pH: 7.5
Staining
Type: NEGATIVE
Material: Uranyl Formate
Grid
Mesh: 400
Model: Maxtaform
Material: COPPER/RHODIUM
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON CONTINUOUS -
Microscopy [1]
Microscope: FEI TECNAI SPIRIT
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 2.2 mm
Nominal defocus: 1.0 µm - 1.5 µm
Calibrated defocus: 0.62 µm - 2.0 µm
Nominal magnification: 52000.0
Calibrated magnification: 52000.0
Specimen holder model: SIDE ENTRY, EUCENTRIC
Alignment procedure: BASIC
Temperature
Minimum: 273.15 K
Maximum: 298.15 K
Image Recording [1]
Detector model: TVIPS TEMCAM-F416 (4k x 4k)
Dimensions: 4096 pixel x 4096 pixel
Sampling interval: 15.6 µm
Number of grids: 1
Number of real images: 590
Average exposure time: 0.42 s
Average electron dose per image: 20.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 29.4 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 6386
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 1.4 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-8899
Details:A negative stain reconstruction of human ATG2-WIPI4 complex was low pass filtered to 60 Angstrom and used as initial model.
⦨ Initial angle assignment
Type: PROJECTION MATCHING
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
Particle selection [1]
Selected Ref. model Method Software Details
37021 - - - -
Final 3D classification
Software [1]
Name Version Details
RELION 1.4 -
CTF correction
Software [1]
Name Version Details
RELION 1.4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Negative stain reconstruction of human ATG2A protein
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 96 96 96
Dimensions (Å) 393.59998 393.59998 393.59998
Voxel size (Å) 4.1 4.1 4.1
Contour list
Primary Level Source
True 5.2 AUTHOR