7RS5

Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules

ELECTRON MICROSCOPY

Sample
Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules
Sample Components
Taxol-stabilized microtubules
yeast kinesin-8/ Kip3

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	14934
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Pseudo-helical symmetry was applied during the reconstruction step
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C14
Axial Rise	8.55
Angular Rotation	-25.76

Map-Model Fitting and Refinement
Id	1 (3JAT, 3JAT, 4FRZ)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Overall correlation of the residues to the map
Overall B Value	100
Fitting Procedure
Details	Multiple rounds of refinement were carried out against one half map (training map), and the other half map (validation map) was used to monitor overfi ...	Multiple rounds of refinement were carried out against one half map (training map), and the other half map (validation map) was used to monitor overfitting based on the procedure described in Wang et al. elife, 2016. It is to note that the molecular interactions of ligand-protein were restrained to the initial poses adapted from the high-resolution structures during structure refinement.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Images were recorded using a semi-automated acquisition program Serial EM with a defocus range from 1.5 to 3.5 um.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Appion
CTF CORRECTION	CTFFIND	4
MODEL FITTING	Rosetta
MODEL REFINEMENT	Rosetta
INITIAL EULER ASSIGNMENT	EMAN2
FINAL EULER ASSIGNMENT	FREALIGN
RECONSTRUCTION	FREALIGN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	The contrast transfer function (CTF) was estimated using CTFFIND4 [(Rohou and Grigorieff, 2015) CTFFIND4: Fast and accurate] with a 500 um step search. A second CTFFIND run with a 100 um step search was carried out to refine the initial defocus values. Micrographs whose estimated resolution was lower than 8 Angstrom with 0.8 confidence were excluded.	67040	Inspection, defocus estimation, microtubule picking, and stack creation were performed within the Appion processing environment (Lander et al., 2009). Images were selected for processing on the basis of high decoration, straight MTs, and the absence of crystalline ice.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.