EMD-2283
Human TFIID Binds to Core Promoter DNA in a Reorganized Structural State
EMD-2283
Single-particle32.0 Å
Deposition: 17/01/2013Map released: 23/01/2013
Last modified: 30/01/2013
Concentration: 0.2
mg/mL
Buffer
pH: 7.8
Details: 20 mM HEPES pH 7.8, 0.2 mM EDTA, 4 mM MgCl2, ~1% glycerol, 1 mM DTT, 3% trehalose, 50 mM KCl, 0.05% NP-40,
Details: 20 mM HEPES pH 7.8, 0.2 mM EDTA, 4 mM MgCl2, ~1% glycerol, 1 mM DTT, 3% trehalose, 50 mM KCl, 0.05% NP-40,
Grid
Details: 400 mesh copper grid on C-flat support carbon with a thin carbon support over 4 um holes space 2 um apart.
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK II
Method: Sample was incubated on grid for 30 seconds before blotting 6.5s at -1 offset. The grid was washed in 4 ul buffer to blot again for 6.5 s at -1 offset prior to plunging.
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK II
Method: Sample was incubated on grid for 30 seconds before blotting 6.5s at -1 offset. The grid was washed in 4 ul buffer to blot again for 6.5 s at -1 offset prior to plunging.
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: 1.8 µm - 4.5 µm
Nominal magnification: 80000.0
Calibrated magnification: 10500.0
Specimen holder model: SIDE ENTRY, EUCENTRIC
Specimen holder details: Gatan 626 liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective and condenser lens astigmatism was corrected at 80,000 times magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 120 kV
Nominal CS: 2.2 mm
Nominal defocus: 1.8 µm - 4.5 µm
Nominal magnification: 80000.0
Calibrated magnification: 10500.0
Specimen holder model: SIDE ENTRY, EUCENTRIC
Specimen holder details: Gatan 626 liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective and condenser lens astigmatism was corrected at 80,000 times magnification, Electron beam tilt params: )
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 1037
Average electron dose per image: 25 e/Å2
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 1037
Average electron dose per image: 25 e/Å2
Details: Particles were prepared within the APPION processing environment. The particles were automatically selected using Signature and extracted from phase flipped micrographs using values calculated by CTFFIND3. After projection matching within EMAN2/Sparx, the final map was further refined in FREALIGN.
Final
reconstruction
Resolution: 32.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 8715
Algorithm: OTHER
Details:
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 8715
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group:
C1
Software
[1]
| Name | Version | Details |
|---|---|---|
| Sparx, EMAN2, FREALIGN | - | - |
CTF correction
Details:Per micrograph for phase flipping, per particles for refinement in FREALIGN
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: 3D reconstruction of canonical conformation of human TFIID in the presence of TFIIA and super core promoter DNA at 32A
Details: ::::EMDATABANK.org::::EMD-2283::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: 3D reconstruction of canonical conformation of human TFIID in the presence of TFIIA and super core promoter DNA at 32A
Details: ::::EMDATABANK.org::::EMD-2283::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 100 | 100 | 100 |
| Origin | 0 | 0 | 0 |
| Spacing | 100 | 100 | 100 |
| Voxel size | 5.48 Å | 5.48 Å | 5.48 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 0.128 | AUTHOR |