Experiment: 6VCC

Cryo-EM structure of the Dvl2 DIX filament

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IW3

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.767
f_angle_d	0.619
f_chiral_restr	0.054
f_plane_restr	0.006
f_bond_d	0.003

Sample
Segment polarity protein dishevelled homolog DVL-2

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	The grid was blotted for 2.0 s using Whatman #1 filter paper (GE Healthcare).

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	110105
Reported Resolution (Å)	3.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	13.5
Angular Rotation	48

Map-Model Fitting and Refinement
Id	1 (6IW3)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The two mutations in the source (Y27W and C80S) were reverted to Trp and Ser, respectively, before fitting. Model refinement was carried out through ...	The two mutations in the source (Y27W and C80S) were reverted to Trp and Ser, respectively, before fitting. Model refinement was carried out through alternating rounds of real-space refinement in PHENIX and manual building in Coot.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	98

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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
Calibrated Magnification	29000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
IMAGE ACQUISITION	DigitalMicrograph
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	PHENIX	1.17.1-3660
INITIAL EULER ASSIGNMENT	RELION	3.0.8
FINAL EULER ASSIGNMENT	RELION	3.0.8
CLASSIFICATION	RELION	3.0.8
RECONSTRUCTION	RELION	3.0.8
MODEL REFINEMENT	PHENIX	1.17.1-3360
MODEL REFINEMENT	Coot	0.8.9.2 EL

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		437872