ELECTRON MICROSCOPY

Sample

Bovine rod PDE6 holoenzyme in complex with the Fab fragment from the ROS-1 monoclonal antibody

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details Applied 3 uL sample per grid and blotted for 1 second before plunging into liquid ethane (FEI VITROBOT MARK III).
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 12373
Reported Resolution (Å) 11.0
Resolution Method FSC 0.143 CUT-OFF
Other Details A total of 21,100 particles were picked from ice images and CTF corrected using Ctfit. After an initial 3D model was generated as described for PDE6, three noise-seeded models were generated and used as initial models in the Multirefine procedure. A model with two Ros-1 Fab bound with a population of ~15,000 particles emerged and was subjected to further refinement using standard iterative projection matching, class averaging, and Fourier reconstruction. The final 3D maps with C2 symmetry were generated from 12,373 particles.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details REFINEMENT PROTOCOL--rigid body DETAILS--Domains were separately fitted by manual docking and Fit in Map in Chimera. The fitting of GFA(A,B) was confirmed using Folderhunter.
Data Acquisition
Detector Type GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å2) 15
Imaging Experiment
Date of Experiment 2011-08-08
Temprature (Kelvin)
Microscope Model JEOL 2010F
Minimum Defocus (nm) ?
Maximum Defocus (nm) ?
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model GATAN LIQUID NITROGEN
Nominal Magnification 60000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details Parallel beam illumination
Imaging Experiment
Task Software Package Version
MODEL FITTING UCSF Chimera ?
RECONSTRUCTION EMAN ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. EMAN ctfit
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