EMD-9902

Subtomogram averaging
23.2 Å
EMD-9902
3D View Gallery
Deposition: 06/05/2019
Map released: 15/04/2020
Last modified: 15/04/2020
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-9902
Download
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)
EMICSS annotations (xml)

S-OPA1 coated liposome tube at GTPgamaS bound state

EMD-9902

Subtomogram averaging
23.2 Å
EMD-9902
3D View Gallery
Deposition: 06/05/2019
Map released: 15/04/2020
Last modified: 15/04/2020
Overview 3D View Sample Experiment Validation Additional data Links
Method: Subtomogram averaging
Aggregation State: Helical Array
Specimen preparation [1]
Concentration: 1 mg/mL
Details: 1mg/ml SOPA1(delta 196-252) was incubated with 1mg/ml liposome at room temperature for 30 min. Then GTPgamaS was added to a final concentration of 1mM, and another 30 min incubation was performed.
Buffer
pH: 8.0
Buffer components [3]:
Name Formula Concentration ChEBI
Tris(hydroxymethyl)aminomethane Tris 20.0 mM
Magnesium chloride MgCl2 1.0 mM
EGTA EGTA 1.0 mM
Grid
Mesh: 300
Model: Quantifoil R2/1
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: OTHER
Support Film [1]
Material Topology Thickness
CARBON HOLEY ARRAY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 289 K
Instrument: FEI VITROBOT MARK IV
Details: The grid was blotted 3.5s with a force 1 before plunging.
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: 50.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 4.0 µm - 6.0 µm
Nominal magnification: 59000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Frames per image: 1-20
Average exposure time: 1.0 s
Average electron dose per image: 3.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 23.2 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 1.4 -
Extraction
Number of images used: 6699
Software [2]
Name Version Details
IMOD 4.9.2 -
RELION 1.4 -
CTF correction
Software [1]
Name Version Details
CTFFIND 4.0.7 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 128 128 128
Dimensions (Å) 348.16 348.16 348.16
Voxel size (Å) 2.72 2.72 2.72
Contour list
Primary Level Source
True 0.14 AUTHOR