7MIZ | pdb_00007miz

Atomic structure of cortical microtubule from Toxoplasma gondii

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FYU
experimental model	PDB	6U42
experimental model	PDB	3JAS

Sample
cortical microtubule with associated MIPs

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	blot for 4 seconds with a blot force of -15

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	220139
Reported Resolution (Å)	3.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4FYU, 6U42, 3JAS)
Refinement Space
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details	Secondary structure, Ramachandran, and rotamer restraints were applied during refinement. The nonbonded_weight value was set to 500 to reduce the clashes between atoms.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	63.7

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	0.01
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

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Appion	3.2
IMAGE ACQUISITION	EPU	1.9.0.30REL
CTF CORRECTION	Gctf	1.18
CTF CORRECTION	RELION	3.1
CTF CORRECTION	cryoSPARC	2.15
MODEL FITTING	Coot	0.8
MODEL REFINEMENT	PHENIX	1.18.2-387464
INITIAL EULER ASSIGNMENT	EMAN	1.9
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
RECONSTRUCTION	cryoSPARC	2.15

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF amplitude correction was performed as part of the 3D reconstruction.	536132	Cortical MTs were manually picked from the motion-corrected micrographs using the APPION image-processing suite. The selected MT segments were computationally cut into overlapping boxes (512x512 pixels) with an 8-nm non-overlapping region (step size) between adjacent boxes (corresponding to the length of a tubulin heterodimer). We refer to these boxed images as 8-nm MT particles.