EMD-10723

Single-particle
8.8 Å
EMD-10723
3D View Gallery
Deposition: 03/03/2020
Map released: 16/09/2020
Last modified: 18/11/2020
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-10723
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3D volume (map.gz) Experimental metadata (xml)
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EMICSS annotations (xml)

OP protein cage

EMD-10723

Single-particle
8.8 Å
EMD-10723
3D View Gallery
Deposition: 03/03/2020
Map released: 16/09/2020
Last modified: 18/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.4
Details: 25 mM Tris-HCl, 200 mM NaCl, 5 mM EDTA, pH 7.4
Grid
Mesh: 400
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 22 K
Details: Blot for 12 s, 25 blot strength, before plunging.
Microscopy [1]
Microscope: FEI TECNAI F20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: -1.8 µm - -3.3 µm
Nominal magnification: 62000.0
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Image Recording [1]
Detector model: FEI FALCON II (4k x 4k)
Detector mode: INTEGRATING
Dimensions: 4096 pixel x 4096 pixel
Frames per image: 1-7
Number of grids: 1
Number of real images: 77
Average electron dose per image: 30.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 8.8 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 2516
⌯ Applied Symmetry
Point group: O
Software [1]
Name Version Details
RELION 3.0 -
Startup model [1]
Type: NONE
Details:The initial model was generated from the data themselves, with octahedral symmetry imposed.
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 3.0 -
Particle selection [1]
Selected Ref. model Method Software Details
45328 - - - -
Final 3D classification
Number of classes: 3
Avg. number of members per classes: 1374.0
Software [1]
Name Version Details
RELION 3.0 -
CTF correction
Software [1]
Name Version Details
Gctf 1.06 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: OP map, postprocessed
⬡ Geometry
X Y Z
Dimensions 180 180 180
Origin 0 0 0
Spacing 180 180 180
Voxel size 1.8 Å 1.8 Å 1.8 Å
Contour list
Primary Level Source
True 0.0857 AUTHOR