EMD-2307
Structural visualization of key steps in human transcription initiation
EMD-2307
Single-particle12.7 Å
Deposition: 05/02/2013
Map released: 13/03/2013
Last modified: 03/04/2013
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
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.
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK II
Method: Incubation on grid for 5 minutes before blotting 4 seconds at -1 offset.
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
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
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 2800
Average electron dose per image: 20 e/Å2
Final
reconstruction
Resolution: 12.7
Å
(
BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 53505
Algorithm: OTHER
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
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::::
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 |