EMD-2427 Experiments and Validation

Negative stain Electron Microscopy of BG505 SOSIP.664 gp140 in complex with PGV04

Single particle reconstruction
Overview of EMD-2427
Sample name: HIV spike protein 664G construct in complex with Fab fragment of PGV04 monoclonal antibody
Organisms: Human immunodeficiency virus, Homo sapiens
Related EM entry by publication: EMD-5723

Map parameters

Recommended contour level: 3.50 (author)
Number of grid points: 96 × 96 × 96
Voxel size: 4.10 × 4.10 × 4.10 Å
Minimum density: -6.326
Maximum density: 14.419
Average density: 0.00
Standard deviation: 0.865

Sample information

Sample name: HIV spike protein 664G construct in complex with Fab fragment of PGV04 monoclonal antibody
Proteins: HIV spike protein BG505 SOSIP.664, PGV04 FAB

Validation information

Experimental information


Image processing

Applied symmetry: C3
Software: EMAN2, EMAN1
Number of particles: 32867
Number of class averages: 256
Reconstruction protocol: common lines
Details: The particles were selected using a DoG Picker, and cleaned using reference free class averaging. The final map was calculated from a single dataset Particles were picked automatically using DoG Picker and put into a particle stack using the Appion software package Initial, reference-free, two-dimensional (2D) class averages were calculated using particles binned by five via the Xmipp Clustering 2D Alignment and sorted into classes. EMAN was used for the 3D reconstruction.


Initial atomic model: 3SE9
Fitting software: Chimera
Fitting protocol: rigid body
Target criteria: Correlation, Fit in Map, Chimera
Refinement space: REAL


Microscope model: FEI TECNAI F20
Electron source: LAB6
Electron dose (e/A**2): 55.0
Nominal CS (mm): 2.00
Nominal magnification: 52000.0
Defocus max (nm): 1,300.00
Defocus min (nm): 900.00
Tilt max (degrees): 50.00
Tilt min (degrees): 0.00
Number of images: 834


Specimen state: particle
Specimen concentration (mg/mL): 0.03
Buffer: 50mM TRIS-HCl 150mM NaCl
Staining procedure: 2% w/v Uranyl Formate for 25 seconds
Specimen support: 400 mesh copper grid
Apparatus: NONE
Cryogen: NONE