7O3H | pdb_00007o3h

Murine CIII2 focus-refined from supercomplex CICIII2

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NTZ
experimental model	PDB	3L75

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.0584
f_angle_d	0.8518
f_chiral_restr	0.0539
f_plane_restr	0.0071
f_bond_d	0.0043

Sample
Murine complex CIII2 focus-refined from supercomplex CICIII2

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	129
Reported Resolution (Å)	2.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details	the final pool of particles was classified without alignment around the MPP cavity to separate the two orientations of Sub 9. the two classes were then refined, first globally and then focused on CIII, re-oriented along the C2 symmetry axis, to allow for subsequent 180 degrees flipping of one class and final re-pooled refinement with all particles having the same orientation of Sub 9
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1NTZ, 3L75)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	MAXIMAL LIKELIHOOD
Overall B Value	65
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	90.66

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
MODEL FITTING	Coot
PARTICLE SELECTION	RELION	3.1
PARTICLE SELECTION	Topaz
CTF CORRECTION	Gctf
CTF CORRECTION	CTFFIND
CTF CORRECTION	RELION	3.1
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1500000	multiple rounds of picking and classification performed, first with Relion LoG and then with Topaz, to extract the best particles from the non-pure starting material