EMD-9309

Single-particle
3.0 Å
EMD-9309
3D View Gallery
Deposition: 06/11/2018
Map released: 13/03/2019
Last modified: 13/03/2024
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EMD-9309
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Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
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EMICSS annotations (xml)

Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction (main population)

EMD-9309

Single-particle
3.0 Å
EMD-9309
3D View Gallery
Deposition: 06/11/2018
Map released: 13/03/2019
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: 3 mg/mL
Buffer
pH: 7.4
Buffer components [3]:
Name Formula Concentration ChEBI
Tris-HCl - 20.0 mM -
Sodium chloride - 50.0 mM -
NP-40 substitute - 0.01 % -
Grid
Mesh: 400
Model: C-flat-1.2/1.3
Material: COPPER
Details: Protochips C-flat 1.2/1.3 holey carbon grids were coated with a thin carbon film and plasma cleaned using a Gatain Solarus.
Pretreatment
Type: PLASMA CLEANING
Atmosphere:
Support Film [2]
Material Topology Thickness
CARBON HOLEY -
CARBON CONTINUOUS -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Details: 5-7 sec incubation of the sample on the grid before blotting and plunging.
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: 50.0 µm
Nominal CS: 2.7 mm
Calibrated defocus: 1.0 µm - 3.5 µm
Calibrated magnification: 48543.0
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3838 pixel x 3710 pixel
Frames per image: 1-30
Number of grids: 1
Number of real images: 928
Average exposure time: 4.5 s
Average electron dose per image: 25.0 e/Å2
Details: 928 images retained after inspection for image quality. Frames were aligned and dose weighed using Motioncor2.
Image processing [1]
Final reconstruction
Resolution: 3.0 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 15779
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: I
Software [1]
Name Version Details
FREALIGN 9 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-8747
Details:The reference was re-scaled and placed in a 512x512x512 voxel box to match the pixel size and appropriate box size for the data.
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: PROJECTION MATCHING
Details: Final refinement in FREALIGN, using defocus refinement and Ewald sphere correction.
Software [1]
Name Version Details
FREALIGN 9 -
Particle selection [1]
Selected Ref. model Method Software Details
31800 - - - 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
Final 3D classification
Number of classes: 4
Avg. number of members per classes: 7950.0
Details: Icosahedral symmetry was applied during the classification.
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 reconstruction of the HO BMC shell (icosahedral symmetry)
⬡ Geometry
X Y Z
Dimensions 512 512 512
Origin 0 0 0
Spacing 512 512 512
Voxel size 1.03 Å 1.03 Å 1.03 Å
Contour list
Primary Level Source
True 0.1 AUTHOR