EMD-2162
Structure of bacteriophage phi29 prohead particle with a double insertion mutation (U92,U93) in the pRNA
EMD-2162
Single-particle17.3 Å
Deposition: 24/07/2012
Map released: 14/08/2013
Last modified: 21/08/2013
Concentration: 0.1
mg/mL
Buffer
pH: 7.8
Details: 25 mM Tris-HCl, 5 mM MgCl2, 50 mM NaCl
Details: 25 mM Tris-HCl, 5 mM MgCl2, 50 mM NaCl
Grid
Details: Quantifoil holey carbon on top of200 mesh copper grid, plasma cleaned
Vitrification
Cryogen name: ETHANE
Instrument: HOMEMADE PLUNGER
Method: Blot grid from behind the sample for ~4 seconds before plunging.
Instrument: HOMEMADE PLUNGER
Method: Blot grid from behind the sample for ~4 seconds before plunging.
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.64 µm - 3.0 µm
Nominal magnification: 60000.0
Calibrated magnification: 60000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 0.64 µm - 3.0 µm
Nominal magnification: 60000.0
Calibrated magnification: 60000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: )
Specialist optics
Energy filter
Name:
JEOL
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 109
Average electron dose per image: 20 e/Å2
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Number of real images: 109
Average electron dose per image: 20 e/Å2
Details: The particles were selected using the model-based automatic particle selection implemented in EMAN, followed by manual deletion of bad particles and manual selection of missed particles
Final
reconstruction
Resolution: 17.3
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 2134
Algorithm: OTHER
Details: C5 symmetry was imposed in all stages of the reconstruction, with the 5-fold axis along Z. The final map was low-pass filtered at 14 angstrom units
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 2134
Algorithm: OTHER
Details: C5 symmetry was imposed in all stages of the reconstruction, with the 5-fold axis along Z. The final map was low-pass filtered at 14 angstrom units
⌯ Applied Symmetry
Point group:
C5
Software
[1]
Name | Version | Details |
---|---|---|
EMAN | - | - |
CTF correction
Details:Each micrograph
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Single particle CryoEM reconstruction of a phi29 prohead particle with a double U92U93 deletion in the pRNA
Details: ::::EMDATABANK.org::::EMD-2162::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Single particle CryoEM reconstruction of a phi29 prohead particle with a double U92U93 deletion in the pRNA
Details: ::::EMDATABANK.org::::EMD-2162::::
⬡ Geometry
X | Y | Z | |
---|---|---|---|
Dimensions | 300 | 300 | 300 |
Origin | -64 | -64 | -64 |
Spacing | 300 | 300 | 300 |
Voxel size | 2.33 Å | 2.33 Å | 2 Å |
Contour list
Primary | Level | Source |
---|---|---|
True | 1.5 | AUTHOR |