8R3Y | pdb_00008r3y

Cryo EM structure of a stable LGL/aPKC Iota/Par-6 complex

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	THIS STUDY
experimental model	PDB	1NF3
experimental model	PDB	6N8Q

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.279
f_angle_d	3.576
f_chiral_restr	0.158
f_bond_d	0.039
f_plane_restr	0.03

Sample
aPKCiota-Par6-Llgl1 complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	4 ul of aPKCiota-Par6-Llgl1 complex at a concentration of 0.4 mg/ml was applied to R1.2/1.3 Quantifoil 300 mesh copper grids which had been glow-discharged for 45 s at 45 mA . Grids were blotted for 2.5 s at 100% humidity using an FEI Vitrobot MK IV.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	121194
Reported Resolution (Å)	3.68
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (8R3X, 1NF3, 6N8Q)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial fitting was done in Chimera. Interactive Model building was done in COOT & Isolde Refinement was done using Phenix.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	48.1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	3000
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

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Xmipp	3
PARTICLE SELECTION	Gautomatch
PARTICLE SELECTION	RELION	3
CTF CORRECTION	CTFFIND	2
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot	0.9.8
MODEL FITTING	ISOLDE
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY		1069057	Semi-automated picking with Xmipp3 and particle extraction in Relion-3 yielded 47,516 particles from 1000 micrographs 38. After reference-free 2D classification in Relion-3, eight 2D classes were selected and used as templates for reference-based particle picking in Gautomatch. A total of particles were extracted with 2-fold binning and submitted to 8 rounds of 2D classification in Relion-3.