EMD-4943

Subtomogram averaging
25.6 Å
EMD-4943
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Deposition: 08/05/2019
Map released: 12/06/2019
Last modified: 25/11/2020
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-4943
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EMICSS annotations (xml)

In situ structure of a pentameric IgM complex bound to complement components C1 and one molecule of C4b

EMD-4943

Subtomogram averaging
25.6 Å
EMD-4943
3D View Gallery
Deposition: 08/05/2019
Map released: 12/06/2019
Last modified: 25/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Details: Antigenic liposomes + IgM + Normal human serum
Buffer
pH: 7.4
Buffer components [1]:
Name Formula Concentration ChEBI
PBS PBS -
Vitrification
Cryogen name: ETHANE
Chamber temperature: 277.15 K
Instrument: LEICA EM GP
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 0.5 µm - 0.5 µm
Nominal magnification: 33000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Specialist optics
Phase plate: VOLTA PHASE PLATE
Energy filter
Name: GIF Quantum LS
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Average exposure time: 2.4 s
Average electron dose per image: 1.48 e/Å2
Details: Exposures of 2.4 sec were dose-fractionated into 6 movie frames per tilt angle. The total dose for each tilt series was 80 e-/A^2. Focusing to -300 nm was performed before each image acquisition using a low-dose routine
Image processing [1]
Details: Raw frames were aligned using alignframes and tomograms were reconstructed using weighted back-projection from the software program IMOD.
Final reconstruction
Resolution: 25.6 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
Dynamo - -
⦩ Final angle assignment
Type: NOT APPLICABLE
Software [1]
Name Version Details
Dynamo - -
Final 3D classification
Number of classes: 3
Software [1]
Name Version Details
Dynamo - -
Extraction
Number of images used: 1522
Software [1]
Name Version Details
EMAN2 2.2 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Pentameric IgM with C1 and one copy of C4b
⬡ Geometry
X Y Z
Dimensions 160 160 160
Origin -80 -80 -80
Spacing 160 160 160
Voxel size 4.3 Å 4.3 Å 4.3 Å
Contour list
Primary Level Source
True 0.5 AUTHOR