ELECTRON MICROSCOPY

Sample

Microtubule decorated with monomeric human kinesin (K349 construct) having ADP aluminum fluoride complex bound in the nucleotide pocket

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details No glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequently, blotting and plunge freezing were performed with ~0.5 second delay after blotting but prior to plunging into liquid ethane.
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 49961
Reported Resolution (Å) 5.0
Resolution Method FSC 0.143 CUT-OFF
Other Details Initial alignment was done using customized SPIDER scripts. Reconstruction and subsequent refinement were done by FREALIGN.
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target RMSD from the starting structure was monitored for convergence.
Overall B Value ?
Fitting Procedure ?
Details REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation, after placing active-site water coordinates identified in high-resolution crystal structures of kinesins ATP-like state. Side chains were excluded from the MDFF target potential. Following several equilibration steps, the relative strength of the EM map potential (GSCALE term) was slowly increased from 0 to 1 over the course of 10 nanoseconds. The t = 1.4 ns time point was selected to represent the final fitted model, based on the approximate convergence of the RMSD from the starting structure.
Data Acquisition
Detector Type GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å2) 15
Imaging Experiment
Date of Experiment 2013-06-02
Temprature (Kelvin)
Microscope Model FEI TITAN
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 LIQUID NITROGEN
Nominal Magnification ?
Calibrated Magnification 23859
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details 4K x 4K counting mode was used. 24 frames total were collected.
Imaging Experiment
Task Software Package Version
MODEL FITTING MDFF ?
RECONSTRUCTION FREALIGN ?
RECONSTRUCTION SPIDER ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. done within FREALIGN
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