7THY | pdb_00007thy

Structure of Leucine Rich Repeat Kinase 2's ROC domain interacting with the microtubule facing the minus end

ELECTRON MICROSCOPY

---

Sample
LRRK2RCKW filament bound to a 11-pf microtubule with MLi-2 present

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	99854
Reported Resolution (Å)	5.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Local refinement done on symmetry expanded helical reconstruction.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Used AlphaFold model as initial model (Q5S007) using only the ROC domain. TUB1 was added to the initial refinement to prevent ROC model from entering density reserved for the microtubule. TUB1 was discarded after the initial refinement.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	55

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	36000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION
IMAGE ACQUISITION	Leginon
CTF CORRECTION	CTFFIND	4
MODEL FITTING	Rosetta	3.13
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	ISOLDE	1.2.2
MODEL REFINEMENT	Rosetta	3.13

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		557577	Filament Autopicker with templates created by manual picking. This is before symmetry expansion.