EMD-2244

Helical reconstruction
9.6 Å
EMD-2244
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Deposition: 18/12/2012
Map released: 20/02/2013
Last modified: 20/04/2016
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EMD-2244
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Cryo-electron microscopy of phirsl1 jumbo phage

EMD-2244

Helical reconstruction
9.6 Å
EMD-2244
3D View Gallery
Deposition: 18/12/2012
Map released: 20/02/2013
Last modified: 20/04/2016
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Helical reconstruction
Aggregation State: Filament
Specimen preparation [1]
Buffer
pH: 7.5
Details: 50 mM Tris-HCl [pH 7.5], 100 mM NaCl, 10 mM MgSO4
Staining
Type: NEGATIVE
Details: Four microliters of the bacteriophage sample (~0.1 mg/ml) were loaded between the mica-carbon interface. The sample was stained using 2% ammonium molybdate pH 7.5 and air-dried.
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: SPOT SCAN
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.3 mm
Nominal defocus: 1.355 µm - 5.295 µm
Nominal magnification: 31000.0
Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 59000, Electron beam tilt params: )
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: ZEISS SCAI
Sampling interval: 7 µm
Number of real images: 52
Average electron dose per image: 20 e/Å2
Bits per pixel: 8.0
Image processing [1]
Details: Projection matching was done with SPIDER. IHRSR was used for helical parameters search and application.
Final reconstruction
Resolution: 9.6 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Algorithm: OTHER
Details:
⌯ Applied Symmetry
ΔΖ: 37.9 Å
ΔΦ: 22.04°
Axial symmetry: C6
Software [1]
Name Version Details
SPIDER, IHRSR - -
CTF correction
Details:Each particle
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of the helical trunk of phirsl1 tail. A Bfactor of -538 has been applied to the reconstruction as well as a soft-edged mask.
Details: ::::EMDATABANK.org::::EMD-2244::::
⬡ Geometry
X Y Z
Dimensions 120 120 120
Origin -3 0 -5
Spacing 120 120 120
Voxel size 2.26 Å 2.26 Å 2.26 Å
Contour list
Primary Level Source
True 0.007 AUTHOR