8QB9 | pdb_00008qb9

Helical reconstruction of yeast eisosome protein Pil1 bound to membrane composed of lipid mixture -PIP2/+sterol (DOPC, DOPE, DOPS, cholesterol 30:20:20:30)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	P53252

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	2.7628
f_angle_d	0.4428
f_chiral_restr	0.0308
f_plane_restr	0.0061
f_bond_d	0.0025

Sample
Helical assembly of recombinant Pil1 protein tubulating -PIP2/+sterol lipid mixture (DOPC,DOPE,DOPS,cholesterol 30:20:20:30)

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	176005
Reported Resolution (Å)	3.35
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	D1
Axial Rise	5.044
Angular Rotation	-136.5
Axial Symmetry	D1
Axial Rise	5.044
Angular Rotation	-136.5

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.1.2
CTF CORRECTION	cryoSPARC	4.1.2
MODEL FITTING	UCSF Chimera	1.16
MODEL FITTING	Coot	0.8.9.2
MODEL REFINEMENT	PHENIX	1.20-4459
INITIAL EULER ASSIGNMENT	cryoSPARC	4.1.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.1.2
RECONSTRUCTION	cryoSPARC	4.1.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION