EMD-5620

Single-particle
34.0 Å
EMD-5620
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Deposition: 22/03/2013
Map released: 24/04/2013
Last modified: 23/04/2014
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5620
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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)
EMICSS annotations (xml)

Outer dynein arm - microtubule complex, biotin-streptavidin tagged at the amino-terminus of the intermediate chain 2.

EMD-5620

Single-particle
34.0 Å
EMD-5620
3D View Gallery
Deposition: 22/03/2013
Map released: 24/04/2013
Last modified: 23/04/2014
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Filament
Specimen preparation [1]
Concentration: 0.03 mg/mL
Buffer
pH: 7.4
Details: 10 mM Hepes-NaOH pH 7.4, 1 mM DTT, 5 mM MgCl2, 1 mM EGTA, 10% trehalose, 0.1% Nonidet P-40, 5 microM paclitaxel
Grid
Details: 400 mesh copper grid with home-made holey carbon support, glow discharged in amylamine atmosphere
Vitrification
Cryogen name: ETHANE
Chamber temperature: 90 K
Instrument: LEICA KF80
Method: Two-side blot by hand for 10 seconds before plunging
Microscopy [1]
Microscope: JEOL 2010F
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 3.3 mm
Nominal defocus: 1.6 µm - 3.3 µm
Nominal magnification: 40000.0
Calibrated magnification: 40000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626 Single Tilt Liquid Nitrogen Cryo Transfer Holder
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification, Electron beam tilt params: )
Temperature
Minimum: 80 K
Average: 95 K
Maximum: 97 K
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: OTHER
Sampling interval: 10 µm
Number of real images: 42
Average electron dose per image: 7 e/Å2
Bits per pixel: 16.0
Image processing [1]
Final reconstruction
Resolution: 34.0 Å ( BY AUTHOR)
Resolution method: FSC 0.33 CUT-OFF
Number of images used: 3350
⌯ Applied Symmetry
ΔΖ: 122.3 Å
ΔΦ: 179.2°
Software [1]
Name Version Details
FREALIGN - -
CTF correction
Details:Wiener filter
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of outer dynein arm-microtubule complex, biotin-streptavidin tagged at the amino-terminus of intermediate chain 2
Details: ::::EMDATABANK.org::::EMD-5620::::
⬡ Geometry
X Y Z
Dimensions 126 186 100
Origin 0 0 0
Spacing 186 126 100
Voxel size 4.87 Å 4.87 Å 4.87 Å
Contour list
Primary Level Source
True 54.1 AUTHOR