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Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket
Sample Components
Human monomeric kinesin-1A construct
Alpha-tubulin
Beta-tubulin
Specimen Preparation
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. Subsequentl ...
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
120783
Reported Resolution (Å)
5
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
Axial Symmetry
C1
Axial Rise
8.78
Angular Rotation
25.77
Map-Model Fitting and Refinement
Id
1 (4HNA, 4HNA, 4HNA)
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. Side chains were excluded from the MDFF target potential. Followi ...
REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit
solvation. 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 = 1.2 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 K2 (4k x 4k)
Electron Dose (electrons/Å**2)
15
Imaging Experiment
1
Date of Experiment
2013-04-15
Temperature (Kelvin)
Microscope Model
FEI TECNAI F30
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
GATAN LIQUID NITROGEN
Nominal Magnification
130000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
8K x 8K super-resolution mode was used. 10 frames total were collected.