EMD-9311 Experiments and Validation

Cryo-EM structure of the HO BMC shell: BMC-T1 in the assembled shell

Single particle reconstruction
Overview of EMD-9311
Sample name: Bacterial microcompartment shell from Haliangium ochraceum
Organisms: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2), Haliangium ochraceum DSM 14365
Fitted atomic model: 6n06

Map parameters

Recommended contour level: 0.03 (author)
Number of grid points: 512 × 512 × 512
Voxel size: 1.03 × 1.03 × 1.03 Å
Minimum density: -0.107
Maximum density: 0.189
Average density: 0.00
Standard deviation: 0.003

Sample information

Sample name: Bacterial microcompartment shell from Haliangium ochraceum
Cellular component: Bacterial microcompartment shell from Haliangium ochraceum
Proteins: Microcompartments protein, Microcompartments protein

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: RELION
Number of particles: 177642
Reconstruction protocol: FOURIER SPACE
CTF correction: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION
Details: The dataset was refined without masking and subsequently masked to reveal only the subregion of the BMC shell to which the focused classification had been applied.

Fitting

Initial atomic models: 5V74, 5DIH
Refinement space: REAL

Imaging

Session
Microscope model: FEI TITAN
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 25.0
Nominal CS (mm): 2.70
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 928
Sampling interval (μm): 5.0
Details: 928 images were retained after inspection for image quality.

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 3.00
Specimen support: Protochips C-flat 1.2/1.3 holey carbon grids were coated with a thin carbon film and plasma-cleaned using a Gatan Solarus.
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Details: 5-7 second incubation of the sample on the grid before blotting and plunging.