EMD-9315 Experiments and Validation

Cryo-EM structure of the HO BMC shell: subregion classified for BMC-T: TS-TDTDTD

Single particle reconstruction
Overview of EMD-9315
Sample name: Bacterial microcompartment shell from Haliangium ochraceum
Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)
Fitted atomic model: 6n0g

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: -0.087
Maximum density: 0.145
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, Microcompartments protein

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: RELION
Number of particles: 80783
Reconstruction protocol: FOURIER SPACE
CTF correction: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION
Details: The selected particle subset 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 retained after inspection for image quality.

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 3.00
Specimen support: unspecified
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.