EMD-2162

Single-particle
17.3 Å
EMD-2162 Deposition: 24/07/2012
Map released: 14/08/2013
Last modified: 21/08/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2162

Structure of bacteriophage phi29 prohead particle with a double insertion mutation (U92,U93) in the pRNA

EMD-2162

Single-particle
17.3 Å
EMD-2162 Deposition: 24/07/2012
Map released: 14/08/2013
Last modified: 21/08/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.1 mg/mL
Buffer
pH: 7.8
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.
Microscopy [1]
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: )
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
Image processing [1]
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
Applied Symmetry
Point group: C5
Software [1]
Name Version Details
EMAN - -
CTF correction
Details:Each micrograph
Map
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::::
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