EMD-8409

Single-particle
3.9 Å
EMD-8409
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Deposition: 12/10/2016
Map released: 26/10/2016
Last modified: 13/03/2024
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EMD-8409
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EMICSS annotations (xml)

Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase

EMD-8409

Single-particle
3.9 Å
EMD-8409
3D View Gallery
Deposition: 12/10/2016
Map released: 26/10/2016
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 2.5 mg/mL
Details: The Vo region was solubilized in amphipol A8-35 (Anatrace)
Buffer
pH: 7.5
Details: 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin
Grid
Mesh: 400
Model: Maxtaform
Material: COPPER/RHODIUM
Pretreatment
Type: GLOW DISCHARGE
Time: {'units': 's', 'valueOf_': '15'}
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
- HOLEY -
Vitrification
Cryogen name: ETHANE-PROPANE
Chamber humidity: 100%
Chamber temperature: 277.3 K
Instrument: FEI VITROBOT MARK III
Details: Modified for ethane/propane.
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Calibrated defocus: 0.8 µm - 3.4 µm
Nominal magnification: 37000.0
Calibrated magnification: 64350.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Details: 70 micro meter objective aperture, illuminated area of 1.58 micro meter diameter
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Number of grids: 1
Number of real images: 4365
Average exposure time: 21.0 s
Average electron dose per image: 100.0 e/Å2
Image processing [1]
Details: Images were recorded in "super-resolution" mode and then resampled by Fourier cropping.
Final reconstruction
Resolution: 3.9 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 462842
Algorithm: FOURIER SPACE
Details: Data beyond 6 A resolution were omitted from refinement.
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
FREALIGN 9.11 -
Startup model [1]
Type: OTHER
Details:An in-house map of the Vo region.
⦨ Initial angle assignment
Type: PROJECTION MATCHING
Merit function: Weighted correlation coefficient
Angular sampling: 3.4 degrees
Details: Frealign exhaustive search (mode 3; i.e. projection matching followed by local refinement of top solutions)
Software [1]
Name Version Details
FREALIGN 9.11 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Merit function: Weighted correlation coefficient
Details: Refinement with Frealign mode 1.
Software [1]
Name Version Details
FREALIGN 9.11 -
Particle selection [1]
Selected Ref. model Method Software Details
657975 - - - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase
⬡ Geometry
X Y Z
Dimensions 200 200 200
Origin 0 0 0
Spacing 200 200 200
Voxel size 1.5539999 Å 1.5539999 Å 1.5539999 Å
Contour list
Primary Level Source
True 0.0475 EMDB