EMD-5455 Experiments and Validation

Cryo-electron tomography of native, trimeric HIV-1 BaL Env in complex with soluble 2-domain CD4

Subtomogram averaging
Overview of EMD-5455
Sample name: Molecular structure of native HIV-1 BaL Env trimer in complex with soluble 2-domain CD4
Organisms: Human immunodeficiency virus 1, Homo sapiens
Related EM entries by publication: EMD-5456, EMD-5457, EMD-5458, EMD-5459, EMD-5460, EMD-5461, EMD-5462

Map parameters

Recommended contour level: 0.18 (author)
Number of grid points: 100 × 100 × 100
Voxel size: 4.10 × 4.10 × 4.10 Å
Minimum density: -0.557
Maximum density: 0.813
Average density: -0.01
Standard deviation: 0.121

Sample information

Sample name: Molecular structure of native HIV-1 BaL Env trimer in complex with soluble 2-domain CD4
Proteins: Envelope glycoprotein, soluble 2-domain CD4

Validation information

Experimental information

 

Image processing

Software: IMOD
Details: Resolution for FSC at 0.5 cut-off is 27 Angstrom Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.

Fitting

Initial atomic model: 1GC1
Used chains: C, G
Fitting software: Chimera
Fitting protocol: rigid body
Refinement space: REAL
Details: Protocol: Rigid body. Automated fitting procedures

Imaging

Session
Microscope model: FEI POLARA 300
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 150.0
Energy filter: GATAN GIF
Energy window (eV): 0.00
Nominal magnification: 34000.0
Defocus max (nm): 2,500.00
Defocus min (nm): 2,500.00
Tilt max (degrees): 60.00
Tilt min (degrees): -60.00
Holder model: GATAN LIQUID NITROGEN

Specimen

Preparation
Buffer: TNE Buffer (10 mM Tris, 150 mM NaCl, 1 mM EDTA)
Specimen support: 200 mesh Quantifoil Multi A
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 100
Protocol: blot for 6 seconds, at 25 degrees C, 100 percent humidity, blot offset of -2, plunge into an ethane slurry cooled by liquid nitrogen