EMD-1906

Tomography
45.0 Å
EMD-1906
Gallery
Deposition: 08/06/2011
Map released: 14/06/2012
Last modified: 02/10/2013
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Overview Sample Experiment Validation Volume Browser Additional data Links

EMD-1906
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Tomographic reconstruction of unstained, frozen-hydrated thylakoid membranes from spinach chloroplasts.

EMD-1906

Tomography
45.0 Å
EMD-1906
Gallery
Deposition: 08/06/2011
Map released: 14/06/2012
Last modified: 02/10/2013
Overview Sample Experiment Validation Volume Browser Additional data Links
Method: Tomography
Specimen preparation [1]
Concentration: 2 mg/mL
Buffer
pH: 6.5
Details: 20mM MES, 5mM MgCl2, 15mM NaCl, pH6.5, 150mM sorbitol.
Staining
Type: NEGATIVE
Details: No stain.
Grid
Details: Quantifoil 400mesh carbon grids with 1.2 micron holes.
Vitrification
Cryogen name: NITROGEN
Chamber humidity: 95%
Chamber temperature: 97 K
Instrument: OTHER
Method: 2 x 1 sec blots before plunging.
Details: Vitrification instrument: Vitrobot FEI. Rapid plunging into liquid ethane.
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 8.0 µm - 8.0 µm
Nominal magnification: 34000.0
Calibrated magnification: 33998.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Single tilt
Alignment procedure: LEGACY (Astigmatism: Astigmatism corrected by live FFT., Electron beam tilt params: )
Temperature
Minimum: 96 K
Average: 97 K
Maximum: 98 K
Image Recording [1]
Sampling interval: 15 µm
Number of real images: 57
Average electron dose per image: 45 e/Å2
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-65 ° 49 ° 1 ° - - - -
Image processing [1]
Details: 1 degree increments above 45 deg, 2.5 degree increments below this.
Final reconstruction
Resolution: 45.0 Å ( BY AUTHOR)
Resolution method: OTHER
Number of images used: 57
Details: Standard eTOMO procedures for single axis tilt tomograms. Fiducials were selected from the tomogram and tracked in each image by hand initially.
Software [1]
Name Version Details
ETOMO - -
CTF correction
Details:None
Tomogram
Format: CCP4
Data type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotation details: Tomographic reconstruction of photosynthetic membranes from spinach chloroplasts resuspended in an isotonic buffer and imaged in an unstained frozen-hydrated state.
Details: ::::EMDATABANK.org::::EMD-1906::::
⬡ Geometry
X Y Z
Dimensions 991 991 161
Origin -1 -1 4
Spacing 991 991 161
Voxel size 17.6 Å 17.6 Å 17.6 Å
Contour list
Primary Level Source
True 150.0 AUTHOR