EMD-5459

Subtomogram averaging
23.0 Å
EMD-5459
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Deposition: 06/08/2012
Map released: 03/10/2012
Last modified: 03/10/2012
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5459
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Cryo-electron tomography of native, trimeric HIV-1 BaL Env in complex with VRC02 Fab

EMD-5459

Subtomogram averaging
23.0 Å
EMD-5459
3D View Gallery
Deposition: 06/08/2012
Map released: 03/10/2012
Last modified: 03/10/2012
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Specimen preparation [1]
Buffer
pH: 7.5
Details: TNE Buffer (10 mM Tris, 150 mM NaCl, 1 mM EDTA)
Grid
Details: 200 mesh Quantifoil Multi A
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 77 K
Instrument: FEI VITROBOT MARK III
Method: blot for 6 seconds, at 25 degrees C, 100 percent humidity, blot offset of -2, plunge into an ethane slurry cooled by liquid nitrogen
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal defocus: 2.5 µm - 2.5 µm
Nominal magnification: 34000.0
Specimen holder model: GATAN LIQUID NITROGEN
Temperature
Average: 81 K
Specialist optics
Energy filter
Name: GATAN GIF
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: CCD
Detector model: GENERIC GATAN
Average electron dose per image: 150 e/Å2
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-60 ° 60 ° - - - - -
Image processing [1]
Details: Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.
Final reconstruction
Resolution: 23.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Details: Resolution for FSC at 0.5 cut-off is 26 Angstrom
Software [1]
Name Version Details
IMOD - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Molecular structure of native HIV-1 BaL Env trimer in complex with VRC02 Fab
Details: ::::EMDATABANK.org::::EMD-5459::::
⬡ Geometry
X Y Z
Dimensions 100 100 100
Origin 0 0 0
Spacing 100 100 100
Voxel size 4.1 Å 4.1 Å 4.1 Å
Contour list
Primary Level Source
True 0.91 AUTHOR