EMD-6746

Single-particle
4.12 Å
EMD-6746
3D View Gallery
Deposition: 26/05/2017
Map released: 14/06/2017
Last modified: 12/02/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-6746
Download
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)
Map and PDB model 5zbo summary report (pdf.gz) Map and 5zbo FULL report (pdf.gz)
EMICSS annotations (xml)

CryoEM structure of PCV2 VLPs

EMD-6746

Single-particle
4.12 Å
EMD-6746
3D View Gallery
Deposition: 26/05/2017
Map released: 14/06/2017
Last modified: 12/02/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 1 mg/mL
Details: This sample was monodisperse
Buffer
pH: 7.0
Buffer components [2]:
Name Formula Concentration ChEBI
Sodium chloride NaCl 500.0 mM
Tris Tris 20.0 mM
Details: 20mM Tris(pH 7.0), 500mM NaCl
Grid
Mesh: 400
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Pressure: 101.325 kPa
Support Film [1]
Material Topology Thickness
FORMVAR HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 298 K
Instrument: FEI VITROBOT MARK IV
Details: Blot for 5 seconds before pluning.
Microscopy [1]
Microscope: FEI TITAN
Illumination mode: OTHER
Imaging mode: DARK FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.0 µm - 3.0 µm
Calibrated defocus: 1.0 µm - 3.0 µm
Nominal magnification: 47000.0
Calibrated magnification: 47000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Details: Preliminary grid screening was performed manually.
Temperature
Minimum: 70.0 K
Maximum: 70.0 K
Image Recording [1]
Detector model: FEI FALCON II (4k x 4k)
Number of grids: 8
Number of real images: 151
Average exposure time: 1.0 s
Average electron dose per image: 25.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 4.12 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 20
Number of images used: 9000
Algorithm: BACK PROJECTION
Software [1]
Name Version Details
RELION 1.4 -
⦨ Initial angle assignment
Type: NOT APPLICABLE
⦩ Final angle assignment
Type: NOT APPLICABLE
Particle selection [1]
Selected Ref. model Method Software Details
20000 - - - -
Final 3D classification
Number of classes: 32
Avg. number of members per classes: 200.0
Software [1]
Name Version Details
RELION 1.4 -
CTF correction
Software [1]
Name Version Details
RELION 1.4 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM structure of full length PCV2 VLPs
⬡ Geometry
X Y Z
Dimensions 200 200 200
Origin 0 0 0
Spacing 200 200 200
Voxel size 1.69 Å 1.69 Å 1.69 Å
Contour list
Primary Level Source
True 0.0929 AUTHOR