EMD-9080

Tomography
100.1 Å
EMD-9080 Deposition: 03/09/2018
Map released: 02/01/2019
Last modified: 25/12/2019
Overview Sample Experiment Validation Volume Browser Additional data Links
Overview Sample Experiment Validation Volume Browser Additional data Links

EMD-9080

Single-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein (No. 12)

EMD-9080

Tomography
100.1 Å
EMD-9080 Deposition: 03/09/2018
Map released: 02/01/2019
Last modified: 25/12/2019
Overview Sample Experiment Validation Volume Browser Additional data Links
Method: Tomography
Aggregation State: Particle
Specimen preparation [1]
Concentration: 2 mg/mL
Details: Human IDLs were isolated from the plasma of a healthy individual by non-equilibrium density gradient ultracentrifugation
Buffer
pH: 7.0
Details: Dulbecco's phosphate buffered saline (DPBS)
Grid
Mesh: 200
Model: Homemade
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON LACEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 80%
Instrument: LEICA EM GP
Sectioning
Details: NO SECTIONING
Microscopy [1]
Microscope: ZEISS LIBRA120PLUS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
Nominal CS: 2.2 mm
Nominal magnification: 50000.0
Alignment procedure: BASIC
Specialist optics
Energy filter
Name: In-column Omega Filter
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Dimensions: 4096 pixel x 4096 pixel
Average electron dose per image: 1.37 e/Å2
Image processing [1]
Details: X-ray speckles in images were removed before CTF correction.
Final reconstruction
Resolution: 100.1 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 35
Algorithm: FOURIER SPACE
Details: The 3D reconstruction was performed by using individual-particle electron tomography (IPET). The obtained 3D map was low-pass filtered to 8 nm.
Tomogram
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Geometry
X Y Z
Dimensions 192 192 192
Origin -96 -96 -96
Spacing 192 192 192
Voxel size 2.4 Å 2.4 Å 2.4 Å
Contour list
Primary Level Source
True - AUTHOR