7RS5
Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules
ELECTRON MICROSCOPY
Sample |
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Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules |
Sample Components |
Taxol-stabilized microtubules |
yeast kinesin-8/ Kip3 |
Specimen Preparation | |
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Sample Aggregation State | HELICAL ARRAY |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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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 | |||||
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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 ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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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. |