EMD-5021

Subtomogram averaging
20.0 Å
EMD-5021
3D View Gallery
Deposition: 29/06/2008
Map released: 05/05/2009
Last modified: 02/08/2011
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5021
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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)
Map and PDB model 3dnl summary report (pdf.gz) Map and 3dnl FULL report (pdf.gz)
EMICSS annotations (xml)

Molecular Structure of the Native HIV-1 gp120 trimer bound to b12: Membrane region

EMD-5021

Subtomogram averaging
20.0 Å
EMD-5021
3D View Gallery
Deposition: 29/06/2008
Map released: 05/05/2009
Last modified: 02/08/2011
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Specimen preparation [1]
Buffer
pH: 7.2
Details: 0.01 M Tris, 0.1 M NaCl, 1 mM EDTA
Grid
Details: Home-made holey carbon
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 77 K
Instrument: OTHER
Method: Blot and plunge
Details: Vitrification instrument: Vitrobot
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.2 mm
Nominal defocus: 2.0 µm - 4.0 µm
Nominal magnification: 34000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Cartridge
Temperature
Average: 77 K
Specialist optics
Energy filter
Name: Gatan
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: CCD
Detector model: GENERIC CCD
Average electron dose per image: 80 e/Å2
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-70 ° 70 ° - - - - -
Image processing [1]
Details: Average number of tilts used in the 3D reconstructions: 400. Average tomographic tilt angle increment: 1.
Final reconstruction
Resolution: 20.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Details:
Software [1]
Name Version Details
IMOD and in-house procedures - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: B12-bound HIV-1 BaL membrane
Details: ::::EMDATABANK.org::::EMD-5021::::
⬡ 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 0.0432 AUTHOR