EMD-2381

Subtomogram averaging
42.0 Å
EMD-2381
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Deposition: 21/05/2013
Map released: 26/06/2013
Last modified: 03/07/2013
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2381
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Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

The structure and super-organization of acetylcholine receptor-rapsyn complexes; class C

EMD-2381

Subtomogram averaging
42.0 Å
EMD-2381
3D View Gallery
Deposition: 21/05/2013
Map released: 26/06/2013
Last modified: 03/07/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.4
Details: 400 mM NaCl, 20 mM phosphate buffer, leupeptin 0.3 mg/l, pepstatin 1 mg/l
Staining
Type: NEGATIVE
Details: Unstained
Grid
Details: 300 mesh copper grid with lacy carbon support, glow discharge in amylamine atmosphere
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 78 K
Instrument: HOMEMADE PLUNGER
Method: blot from the carbon side
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2 mm
Nominal defocus: 3.0 µm - 6.0 µm
Nominal magnification: 69000.0
Calibrated magnification: 80213.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 69,000 times magnification, Electron beam tilt params: )
Details: Dual tilt axis tomography
Temperature
Minimum: 80 K
Average: 85 K
Maximum: 95 K
Specialist optics
Energy filter
Name: Gatan
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Number of real images: 142
Average electron dose per image: 50 e/Å2
Bits per pixel: 16.0
Details: Dual axis tilt series
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-70 ° 70 ° - - - - -
Image processing [2]
Final reconstruction
Algorithm: OTHER
Software [1]
Name Version Details
IMOD, PRIISM/IVE - -
Final 3D classification
Number of classes: 5
Final reconstruction
Resolution: 42.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Algorithm: OTHER
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
XMIPP, ML, TOMO - -
Final 3D classification
Number of classes: 5
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Acetylcholine receptor with two pairs of rapsyn bound at approximately 72 degrees apart
Details: ::::EMDATABANK.org::::EMD-2381::::
⬡ Geometry
X Y Z
Dimensions 60 60 60
Origin 0 0 0
Spacing 60 60 60
Voxel size 7.48 Å 7.48 Å 7.48 Å
Contour list
Primary Level Source
True 0.248 AUTHOR