EMD-3916

Subtomogram averaging
11.8 Å
EMD-3916
3D View Gallery
Deposition: 11/10/2017
Map released: 07/02/2018
Last modified: 11/12/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-3916
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 6epf summary report (pdf.gz) Map and 6epf FULL report (pdf.gz)
EMICSS annotations (xml)

Ground state 26S proteasome (GS1)

EMD-3916

Subtomogram averaging
11.8 Å
EMD-3916
3D View Gallery
Deposition: 11/10/2017
Map released: 07/02/2018
Last modified: 11/12/2019
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Cell
Specimen preparation [1]
Details: FIB milled rat primary neurons
Buffer
pH: 7.0
Grid
Mesh: 200
Model: Quantifoil R2/1
Material: GOLD
Details: The grid was coated with C prior to use
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE-PROPANE
Chamber humidity: 100%
Chamber temperature: 298 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
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: 5.0 µm - 7.0 µm
Nominal magnification: 42000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Average exposure time: 2.4 s
Average electron dose per image: 1.8 e/Å2
Image processing [1]
Final reconstruction
Resolution: 11.8 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Software [1]
Name Version Details
RELION 1.4 -
Final 3D classification
Number of classes: 4
Software [1]
Name Version Details
RELION 1.4 -
Extraction
Number of images used: 10367
Reference model: Average of manual picked subtomograms
Method: Template matching
Software [3]
Name Version Details
PyTom - -
TOM Toolbox - -
RELION 1.4 -
CTF correction
Software [2]
Name Version Details
CTFFIND - -
RELION 1.4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: In situ reconstruction of Rat proteasome in Ground State 1
⬡ Geometry
X Y Z
Dimensions 90 90 90
Origin -44 -44 -44
Spacing 90 90 90
Voxel size 3.4200003 Å 3.4200003 Å 3.4200003 Å
Contour list
Primary Level Source
True 0.4 AUTHOR