EMD-2307

Single-particle
12.7 Å
EMD-2307 Deposition: 05/02/2013
Map released: 13/03/2013
Last modified: 03/04/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2307

Structural visualization of key steps in human transcription initiation

EMD-2307

Single-particle
12.7 Å
EMD-2307 Deposition: 05/02/2013
Map released: 13/03/2013
Last modified: 03/04/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.09 mg/mL
Buffer
pH: 7.9
Details: 10 mM HEPES, 5% glycerol, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 0.05% NP-40
Grid
Details: 400-mesh C-flats with thin carbon support over 4um holes with 2um spacing (Protochips Inc.)
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK II
Method: Incubation on grid for 5 minutes before blotting 4 seconds at -1 offset.
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 120 kV
Nominal CS: 2.2 mm
Nominal defocus: 1.2 µm - 2.4 µm
Nominal magnification: 100000.0
Calibrated magnification: 100000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626 liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification., Electron beam tilt params: )
Details: Data acquired using Leginon
Image Recording [1]
Detector category: CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 2800
Average electron dose per image: 20 e/Å2
Image processing [1]
Final reconstruction
Resolution: 12.7 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 53505
Algorithm: OTHER
Applied Symmetry
Point group: C1
Software [1]
Name Version Details
EMAN2, SPARX - -
CTF correction
Details:Whole micrograph
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: TBP-TFIIA-TFIIB-DNA-Pol II-TFIIF-TFIIE (open)
Details: ::::EMDATABANK.org::::EMD-2307::::
Geometry
X Y Z
Dimensions 192 192 192
Origin 0 0 0
Spacing 192 192 192
Voxel size 2.1 Å 2.1 Å 2.1 Å
Contour list
Primary Level Source
True 1.3 AUTHOR