EMD-5668
26S proteasome Rpn11AXA Rpn13-delta mutant
EMD-5668
Single-particle9.0 Å
Deposition: 08/05/2013Map released: 19/06/2013
Last modified: 17/07/2013
Concentration: 2
mg/mL
Buffer
pH: 7.6
Details: 60mM HEPES, 50mM NaCl, 50mM KCl, 5mM MgCl2, 0.5mM EDTA, 1mM DTT, 2mM ATP, 0.05% NP40
Details: 60mM HEPES, 50mM NaCl, 50mM KCl, 5mM MgCl2, 0.5mM EDTA, 1mM DTT, 2mM ATP, 0.05% NP40
Grid
Details: 400-mesh C-flats, 2 um holes with 2 um spacing (Protochips Inc.)
Vitrification
Cryogen name: ETHANE
Chamber humidity: 50%
Chamber temperature: 86 K
Instrument: FEI VITROBOT MARK II
Method: Blot 3 seconds with -1 offset
Chamber humidity: 50%
Chamber temperature: 86 K
Instrument: FEI VITROBOT MARK II
Method: Blot 3 seconds with -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 - 2.5 µm
Nominal magnification: 100000.0
Calibrated magnification: 100000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626, 70 degree cryoholder
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification, Electron beam tilt params: )
Details: Data acquired with 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 - 2.5 µm
Nominal magnification: 100000.0
Calibrated magnification: 100000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626, 70 degree cryoholder
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification, Electron beam tilt params: )
Details: Data acquired with Leginon
Temperature
Minimum: 78
K
Average: 79 K
Maximum: 80 K
Average: 79 K
Maximum: 80 K
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 4740
Average electron dose per image: 20 e/Å2
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 4740
Average electron dose per image: 20 e/Å2
Details: 3D reconstruction with EMAN2/SPARX libraries; final alignment of particles with FREALIGN. Sharpened with SPIDER; low-pass filtered to local resolution with BSOFT.
Final
reconstruction
Resolution: 9.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 80011
Algorithm: OTHER
Details: Final map filtered to local resolution using the blocfilt function in Bsoft. Image processing performed in the Appion processing environment.
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 80011
Algorithm: OTHER
Details: Final map filtered to local resolution using the blocfilt function in Bsoft. Image processing performed in the Appion processing environment.
⌯ Applied Symmetry
Point group:
C2
Software
[1]
| Name | Version | Details |
|---|---|---|
| EMAN2/SPARX, FREALIGN | - | - |
CTF correction
Details:Each particle
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of the Rpn11AXA Rpn13-delta yeast 26S proteasome in the absence of substrate
Details: ::::EMDATABANK.org::::EMD-5668::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of the Rpn11AXA Rpn13-delta yeast 26S proteasome in the absence of substrate
Details: ::::EMDATABANK.org::::EMD-5668::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 240 | 240 | 240 |
| Origin | 40 | 40 | 40 |
| Spacing | 240 | 240 | 240 |
| Voxel size | 2.1700003 Å | 2.1700003 Å | 2.1700003 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 2.0 | AUTHOR |