ELECTRON MICROSCOPY

Sample

Bor1p dimer in an inward-facing conformation

Specimen Preperation
Sample Aggregation State HELICAL ARRAY
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 75
Reported Resolution (Å) 5.9
Resolution Method FSC 0.143 CUT-OFF
Other Details Reconstruction was done using D1 symmetry because of an existing two-fold symmetry in the unit cells composing the helical lattice. This two-fold axis runs perpendicular to the helical axis. For the final structure, a filter was applied to the map in order to compensate for resolution-dependent amplitude falloff. To do so, we built a model by arranging UraA in a helical assembly in order to mimic the mass distribution in Bor1p tubes. Fourier transforms from this model and from the experimental maps were then rotationally averaged to produce 1D scattering profiles. The resolution-dependent amplitude ratio from these profiles was used as a filter that was applied to the experimental amplitudes using SPARX routines. Finally, a low-pass filter was applied with a 5 Angstrom stop-band frequency.
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details A homology model was first created using human AE1 (PDB entry 4YZF) as a template using MODELLER, placed into the density map using SITUS, and then fitted into the map using the Molecular Dynamics Flexible Fitting (MDFF) method.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 45
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 2500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification 19000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION SPARX/EMAN2 EMAN2.1
CTF CORRECTION CTFFIND 3
CTF CORRECTION FREALIX 1.2.0
MODEL FITTING Situs 2.8
MODEL FITTING NAMD 2.11
INITIAL EULER ASSIGNMENT FREALIX 1.2.0
FINAL EULER ASSIGNMENT FREALIX 1.2.0
RECONSTRUCTION FREALIX 1.2.0
RECONSTRUCTION SPARX/EMAN2 EMAN2.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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