5M5O

ELECTRON MICROSCOPY

Sample

microtubule-bound S. pombe kinesin-5 motor domain in the AMPPNP state

Specimen Preperation
Sample Aggregation State HELICAL ARRAY
Vitrification Instrument FEI VITROBOT MARK I
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 144300
Reported Resolution (Å) 9.3
Resolution Method FSC 0.5 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details An initial homology model of S. pombe cut7 kinesin-5 motor domain based on human kinesin-5 structure (PDB 3HQD) was prepared using Modeller. The coordinates of motor bound to an alpha-beta tubulin dimer (PDB 1JFF) were rigidly fitted into the cryo-EM map using Chimera and refined by flexible fitting using Flex-EM. Structural models of loop5 and loop10 were generated using Modeller. The conformation of the neck-linker and the N-terminus were calculated using a conjugate-gradient energy minimization approach.
Data Acquisition
Detector Type GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å2) 20
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 700
Maximum Defocus (nm) ?
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification ?
Calibrated Magnification 68000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION EMAN ?
CTF CORRECTION CTFFIND 3
CTF CORRECTION FREALIGN ?
MODEL FITTING UCSF Chimera ?
MODEL FITTING Flex-EM ?
INITIAL EULER ASSIGNMENT SPIDER ?
FINAL EULER ASSIGNMENT FREALIGN ?
RECONSTRUCTION FREALIGN ?
MODEL REFINEMENT Flex-EM ?
MODEL REFINEMENT MODELLER ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?