EMD-4015

Subtomogram averaging
3.9 Å
EMD-4015
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Deposition: 09/06/2016
Map released: 13/07/2016
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-4015
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A 3.9 Angstrom structure of HIV-1 CA-SP1 assembled in presence of Bevirimat

EMD-4015

Subtomogram averaging
3.9 Å
EMD-4015
3D View Gallery
Deposition: 09/06/2016
Map released: 13/07/2016
Last modified: 15/05/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Concentration: 5 mg/mL
Details: Virus-like particles were assembled in vitro
Buffer
pH: 8.0
Buffer components [4]:
Name Formula Concentration ChEBI
HEPES - 50.0 mM -
Sodium Chloride NaCl 100.0 mM
EDTA - 1.0 mM -
TCEP - 1.0 mM -
Details: Virus-like particles were assembled in the presence of nucleic acid (73mer oligonucleotide, 1:10 molar ratio oligonucleotide:protein).
Grid
Mesh: 300
Model: C-flat
Material: COPPER
Details: At 20 mA
Pretreatment
Type: GLOW DISCHARGE
Time: 30 s
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 15 K
Instrument: FEI VITROBOT MARK II
Details: 10nM colloidal gold was added to the sample prior to plunge freezing..
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: 1.5 µm - 5.0 µm
Nominal magnification: 105000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: ZEMLIN TABLEAU
Details: Nanoprobe
Specialist optics
Energy filter
Name: GIF Quantum LS
Lower energy threshold: 0 eV
Upper energy threshold: 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: 8-10
Number of grids: 2
Average exposure time: 1.0 s
Average electron dose per image: 3.4 e/Å2
Details: Number of frames ranged from 8-10 Exposure time per tilt ranged from 0.8 to 1.0 seconds
Image processing [1]
Details: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
Final reconstruction
Resolution: 3.9 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Details:
⌯ Applied Symmetry
Point group: C6
Software [2]
Name Version Details
AV3 - -
TOM Toolbox - -
⦩ Final angle assignment
Type: OTHER
Details: Cross-correlation based template matching
Software [2]
Name Version Details
AV3 - -
TOM Toolbox - -
Extraction
Number of images used: 527528
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
⬡ 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 0.112 AUTHOR