EMD-8972

Single-particle
3.5 Å
EMD-8972
3D View Gallery
Deposition: 12/07/2018
Map released: 26/12/2018
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8972
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 6e30 summary report (pdf.gz) Map and 6e30 FULL report (pdf.gz)
EMICSS annotations (xml)

Mechanism of cellular recognition by PCV2

EMD-8972

Single-particle
3.5 Å
EMD-8972
3D View Gallery
Deposition: 12/07/2018
Map released: 26/12/2018
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.718 mg/mL
Details: This sample was monodisperse
Buffer
pH: 7.0
Buffer components [4]:
Name Formula Concentration ChEBI
(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) HEPES 20.0 mM
Sodium Chloride NaCl 250.0 mM
Tris(2-carboxyethyl)phosphine TCEP 0.1 mM
Ethylenediaminetetraacetic acid EDTA 2.0 mM
Grid
Material: COPPER
Details: Unspecified
Support Film [1]
Material Topology Thickness
CARBON LACEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 4 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: FEI TITAN
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 100.0 µm
Nominal CS: 0.01 mm
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Frames per image: 2-25
Number of grids: 1
Number of real images: 3725
Average exposure time: 5.0 s
Average electron dose per image: 32.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 3.5 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of images used: 74170
Software [1]
Name Version Details
FREALIGN 9.11 No refinement of parameters
Startup model [1]
Type: PDB ENTRY
PDB model: 3R0R
Details:Low pass filtered to 60 Angstroms
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION - -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION - -
Particle selection [1]
Selected Ref. model Method Software Details
166369 - - - -
Final 3D classification
Number of classes: 1
Software [1]
Name Version Details
FREALIGN 9,11 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Porcine Circovirus 2, primary map
⬡ Geometry
X Y Z
Dimensions 300 300 300
Origin 0 0 0
Spacing 300 300 300
Voxel size 1.09 Å 1.09 Å 1.09 Å
Contour list
Primary Level Source
True 0.02 AUTHOR