EMD-1951 Experiments and Validation

Structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism

Helical reconstruction
Overview of EMD-1951
Sample name: CS1 pilus
Organism: Escherichia coli
Fitted atomic model: 3s0v
Related EM entry by publication: EMD-1952, EMD-1953

Map parameters

Recommended contour level: 4.16 (author)
Number of grid points: 100 × 100 × 100
Voxel size: 4.16 × 4.16 × 4.16 Å
Minimum density: -1,775.237
Maximum density: 2,061.08
Average density: 3.499
Standard deviation: 173.969

Sample information

Sample name: CS1 pilus
Cellular component: CooA

Validation information

Experimental information

 

Image processing

Software: SPIDER, IHRSR
Reconstruction protocol: Single particle reconstruction

Fitting

Initial atomic model: 3S0V
Used chain: 3S0V_A
Fitting protocol: rigid body
Refinement space: REAL
Details: Protocol: Rigid body. A single subunit was manually docked using CHIMERA and the filament was built by applying the symmetry parameters for the reconstruction.

Imaging

Session
Microscope model: FEI TECNAI 12
Electron source: LAB6
Electron dose (e/A**2): 10.0
Nominal CS (mm): 2.00
Nominal magnification: 30000.0
Defocus max (nm): 2,000.00
Defocus min (nm): 1,000.00
Holder model: SIDE ENTRY, EUCENTRIC
Details: Low dose mode
Acquisition
Number of images: 10
Scanner model: NIKON COOLSCAN
Sampling interval (μm): 4.1600000000000001

Specimen

Preparation
Specimen state: filament
Specimen concentration (mg/mL): 0.20
Buffer: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, 10 mM EDTA
Staining procedure: 2% uranyl acetate
Specimen support: glow discharged continuous carbon coated grids
Aggregation parameters (helical parameters)
Handedness: RIGHT HANDED
Phi increment (degrees): 113.0
Azimuthal (Z) increment (Å): 8.6999999999999993
Vitrification
Apparatus: NONE
Cryogen: NONE