EMD-5526 Experiments and Validation

Electron cryo-microscopy of ABC BmrA in 13-fold symmetry rings

Single particle reconstruction
Overview of EMD-5526
Sample name: BmrA reconstituted at high density into lipid bilayer.
Organism: Bacillus subtilis
Related EM entry by publication: EMD-5525

Map parameters

Minimum density: -0.03
Maximum density: 0.05
Average density: 0
Standard deviation: 0.01
Recommended contour level: 0.02 (author)

Sample information

Sample name: BmrA reconstituted at high density into lipid bilayer.
Protein: BmrA

Validation information

Experimental information

 

Image processing

Applied symmetry: D13
Software: Xmipp
Number of particles: 1229
Reconstruction protocol: Projection matching refinement
CTF correction: Micrograph based

Fitting

Initial atomic model: 3G61
Fitting software: Chimera
Fitting protocol: rigid body
Target criteria: Cross correlation factor
Refinement space: REAL
Details: Protocol: Rigid body

Imaging

Session
Microscope model: FEI/PHILIPS CM200FEG
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 15.0
Nominal CS (mm): 2.26
Nominal magnification: 50000.0
Defocus max (nm): 5,000
Defocus min (nm): 2,600
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 102
Scanner model: NIKON COOLSCAN

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.1
Buffer: 50mM HEPES, 100mM NaCl
Specimen support: Ted Pella inc. holey formvar grid
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Protocol: Blot for 3 seconds before plunging.
Details: specimen linked to a Ni++-NTA-DOGS/DOPC lipid monolayer