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PDB Id
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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9YAB
pdb_00009yab
10.2210/pdb9yab/pdb
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ELECTRON MICROSCOPY
Sample
KIF1A R350W bound to microtubules in the apo state
Specimen Preperation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 0.005 units per uL apyrase was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane.
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
953398
Reported Resolution (Å)
3.21
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
?
Overall B Value
104.8
Fitting Procedure
?
Details
?
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å
2
)
57.96
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
90
Maximum Defocus (nm)
2300
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.6.0
MODEL FITTING
UCSF Chimera
?
MODEL FITTING
Rosetta
?
MODEL REFINEMENT
PHENIX
?
CLASSIFICATION
cryoSPARC
4.6.0
RECONSTRUCTION
cryoSPARC
4.6.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
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