EMD-5453

Subtomogram averaging
60.0 Å
EMD-5453
3D View Gallery
Deposition: 30/07/2012
Map released: 17/10/2012
Last modified: 24/10/2012
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5453
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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)

A Tail-like Assembly at the Portal Vertex in Intact Herpes Simplex Type-1 Virions

EMD-5453

Subtomogram averaging
60.0 Å
EMD-5453
3D View Gallery
Deposition: 30/07/2012
Map released: 17/10/2012
Last modified: 24/10/2012
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.2
Details: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 4.9mM MgCl2, 6.8mM CaCl2
Grid
Details: Quantifoil R 2/2 holey carbon film on a 200 mesh copper grid, glow discharged in air
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Chamber temperature: 120 K
Instrument: FEI VITROBOT MARK IV
Method: Manual blotting
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 mm
Nominal defocus: 4.0 µm - 4.0 µm
Nominal magnification: 20000.0
Calibrated magnification: 28195.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 914
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: )
Temperature
Average: 100 K
Specialist optics
Energy filter
Name: Omega
Lower energy threshold: 25.0 eV
Upper energy threshold: 30.0 eV
Image Recording [1]
Detector category: FILM
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Scanner: OTHER
Sampling interval: 15 µm
Number of real images: 11
Average electron dose per image: 88 e/Å2
Bits per pixel: 16.0
Tilt Series [1]
Axis 1 Axis 2
Min. Max. Inc. Min. Max. Inc. Rotation
-60 ° 60 ° - - - - -
Image processing [1]
Details: Multivariate Statistical Analysis (MSA) was used to classify a unique vertex in the capsid shell for alignment and averaging. Further details provided in manuscript. Average number of projections used in the 3D reconstructions: 214.
Final reconstruction
Resolution: 60.0 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Algorithm: OTHER
Details: Final map is the average of 214 subvolumes
Software [1]
Name Version Details
IMOD, tomohunter - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of HSV-1 virion using Melon Ball alignment
Details: ::::EMDATABANK.org::::EMD-5453::::
⬡ Geometry
X Y Z
Dimensions 350 350 350
Origin -175 -175 -175
Spacing 350 350 350
Voxel size 10.8 Å 10.8 Å 10.8 Å
Contour list
Primary Level Source
True 4.35 AUTHOR