EMD-1048 Experiments and Validation

Three-dimensional structure of bacteriophage T4 baseplate.

Single particle reconstruction
Overview of EMD-1048
Sample name: Bacteriophage T4 baseplate-tail tube assembly
Organism: Enterobacteria phage T4
Fitted atomic models: 1pdf, 1pdi, 1pdj, 1pdl, 1pdm, 1pdp, 2fl8, 3h3w

Map parameters

Minimum density: -7.648
Maximum density: 10.345
Average density: 0.00
Standard deviation: 1.00
Recommended contour level: 1.45 (author)

Sample information

Sample name: Bacteriophage T4 baseplate-tail tube assembly
Protein: baseplate-tail tube complex

Validation information

Experimental information

 

Image processing

Applied symmetry: C6
Software: SPIDER
Number of particles: 945
Reconstruction protocol: model based projection matching
CTF correction: each particle
Details: modified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly

Fitting

Fitting 1
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 2
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 3
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 4
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 5
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 6
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 7
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space
Fitting 8
Fitting software: Situs 2.0, Colores
Fitting protocol: rigid body
Target criteria: correlation coefficient
Refinement space: REAL
Details: Protocol: laplacian filtered real space

Imaging

Session
Microscope model: FEI/PHILIPS CM300FEG/T
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 25.0
Nominal CS (mm): 2.00
Nominal magnification: 45000.0
Defocus max (nm): 5,000.00
Defocus min (nm): 1,200.00
Tilt max (degrees): 0.00
Tilt min (degrees): 0.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 15
Scanner model: ZEISS SCAI
Sampling interval (μm): 14.0
Details: images were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 5.00
Buffer: water
Specimen support: holey carbon
Vitrification
Cryogen: ETHANE
Protocol: Blot for 2 seconds before plunging