EMD-3816
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC2
EMD-3816
Single-particle3.6 Å
Deposition: 18/07/2017Map released: 13/09/2017
Last modified: 06/11/2019
Concentration: 0.25
mg/mL
Buffer
pH: 7.25
Buffer components [4]:
Details: PH was adjusted at 25 degrees Celsius
Buffer components [4]:
| Name | Formula | Concentration | ChEBI |
|---|---|---|---|
| HEPES | - | 5.0 mM | - |
| Sodium chloride | NaCl | 150.0 mM | |
| Zinc chloride | ZnCl2 | 0.01 mM | |
| Dithiothreitol | - | 1.0 mM | - |
Grid
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Details: Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane..
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Details: Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane..
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.6 µm - 3.6 µm
Calibrated defocus: 0.6 µm - 3.6 µm
Nominal magnification: 37000.0
Calibrated magnification: 37037.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.6 µm - 3.6 µm
Calibrated defocus: 0.6 µm - 3.6 µm
Nominal magnification: 37000.0
Calibrated magnification: 37037.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Specialist optics
Energy filter
Image Recording
[1]
Detector model:
GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Frames per image: 1-33
Number of grids: 1
Number of real images: 2549
Average exposure time: 9.9 s
Average electron dose per image: 33.0 e/Å2
Details: Movies were aligned and binned to the physical pixel size of 1.35 angstroms.
Detector mode: SUPER-RESOLUTION
Frames per image: 1-33
Number of grids: 1
Number of real images: 2549
Average exposure time: 9.9 s
Average electron dose per image: 33.0 e/Å2
Details: Movies were aligned and binned to the physical pixel size of 1.35 angstroms.
Final
reconstruction
Resolution: 3.6
Å
(
BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 139075
Algorithm: FOURIER SPACE
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 139075
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group:
C1
Software
[1]
| Name | Version | Details |
|---|---|---|
| RELION | 1.4 | - |
⦨ Initial angle
assignment
⦩ Final angle assignment
Particle selection
[1]
| Selected | Ref. model | Method | Software | Details |
|---|---|---|---|---|
| 687928 | - | - | - | - |
CTF correction
Software
[1]
| Name | Version | Details |
|---|---|---|
| CTFFIND | 4.0.16 | - |
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: None
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: None
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 256 | 256 | 256 |
| Origin | 0 | 0 | 0 |
| Spacing | 256 | 256 | 256 |
| Voxel size | 1.35 Å | 1.35 Å | 1.35 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 0.04 | AUTHOR |