EMD-2309 Experiments and Validation

Structural visualization of key steps in human transcription initiation

Single particle reconstruction
Overview of EMD-2309
Sample name: apo TFIIH
Organism: Homo sapiens
Related EM entries by publication: EMD-2304, EMD-2305, EMD-2306, EMD-2307, EMD-2308

Map parameters

Recommended contour level: 2.40 (author)
Number of grid points: 128 × 128 × 128
Voxel size: 2.56 × 2.56 × 2.56 Å
Minimum density: -4.915
Maximum density: 14.35
Average density: 0.00
Standard deviation: 1.00

Sample information

Sample name: apo TFIIH
Protein: General transcription factor IIH

Validation information

Experimental information


Image processing

Applied symmetry: C1
Software: EMAN2, SPARX
Number of particles: 13023
Reconstruction protocol: Projection matching
CTF correction: whole micrograph
Details: Image processing was performed in the Appion processing environment. 3D reconstruction was performed using EMAN2 and SPARX libraries. Final map was filtered to local resolution using the blocres function in Bsoft package.


Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Nominal CS (mm): 2.20
Nominal magnification: 80000.0
Defocus max (nm): 1,200.00
Defocus min (nm): 500.00
Details: Data acquired using Leginon
Number of images: 450


Specimen state: particle
Specimen concentration (mg/mL): 0.04
Buffer: 10 mM HEPES, 5% glycerol, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 0.05% NP-40
Staining procedure: Grids with adsorbed protein floated on 2% w/v uranyl formate for 1 minute.
Specimen support: 200 mesh Cu grid
Apparatus: NONE
Cryogen: NONE