EMD-5260

Single-particle
24.0 Å
EMD-5260
3D View Gallery
Deposition: 16/02/2011
Map released: 10/03/2011
Last modified: 16/04/2014
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5260
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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)

Seeing the Portal in Herpes Simplex Virus type I B-capsids.

EMD-5260

Single-particle
24.0 Å
EMD-5260
3D View Gallery
Deposition: 16/02/2011
Map released: 10/03/2011
Last modified: 16/04/2014
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Grid
Details: Quantifoil 2/2 grids
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 85 K
Instrument: FEI VITROBOT MARK IV
Method: Blot 1 time for 2 seconds
Details: Vitrification instrument: Vitrobot Mark IV
Microscopy [1]
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 4.1 mm
Nominal defocus: 0.0 µm - 0.2 µm
Nominal magnification: 40000.0
Calibrated magnification: 56000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side Entry
Alignment procedure: LEGACY (Astigmatism: Astigmatism was corrected at 400,000 times magnification, Electron beam tilt params: )
Minimum tilt angle: 0
Maximum tilt angle: 0
Temperature
Minimum: 100 K
Average: 100 K
Maximum: 101 K
Specialist optics
Energy filter
Name: Omega
Lower energy threshold: 0.0 eV
Upper energy threshold: 20.0 eV
Image Recording [1]
Detector category: CCD
Detector model: GENERIC TVIPS (4k x 4k)
Average electron dose per image: 20 e/Å2
Image processing [1]
Details: The particles were aligned using the multi-path simulated annealing algorithm.
Final reconstruction
Resolution: 24.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 6300
Algorithm: OTHER
Details: Reconstructions were made both with and without imposed symmetry.
⌯ Applied Symmetry
Point group: C12
Software [1]
Name Version Details
MPSA - -
CTF correction
Details:No Correction
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: C12 symmetrized portal density extracted from symmetry free (c1) reconstruction of the HSV-1 B-capsid
Details: ::::EMDATABANK.org::::EMD-5260::::
⬡ Geometry
X Y Z
Dimensions 300 300 300
Origin -144 -144 -144
Spacing 300 300 300
Voxel size 5.32 Å 5.32 Å 5.32 Å
Contour list
Primary Level Source
True 2.0 AUTHOR