ELECTRON MICROSCOPY

Sample

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

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details Applied 3 uL of 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 21100 particles were picked from ice images and CTF-corrected using Ctfit. Initial three-dimensional models were generated from either reference-free class averages or from a cylinder. The two models were essentially similar. Three noise-seeded models were generated and used as initial models in Multirefine. A model with two Ros-1 Fabs bound emerged from a population of 15000 particles and was subjected to further refinement using standard iterative projection matching, class averaging, and Fourier reconstruction. The final three-dimensional map with C2 symmetry was generated from 12373 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 refinement DETAILS--The domains were fit using Chimera. The model was refined using Phenix real-space refinement.
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 PHENIX ?
MODEL FITTING UCSF Chimera ?
RECONSTRUCTION EMAN ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. by particle using CtFit