Experiment: 6W17

Structure of Dip1-activated Arp2/3 complex with nucleated actin filament

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DWL
experimental model	PDB	3J8I
experimental model	PDB	6D8C

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.5994
f_angle_d	0.5516
f_chiral_restr	0.0409
f_plane_restr	0.0025
f_bond_d	0.0022

Sample
Complex consisting of actin-filament nucleator, Arp2/3 complex associated with nucleation promoting factor Dip1 and first four actin subunits from the pointed end of the nucleated actin-filament

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	110433
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3DWL, 3J8I, 6D8C)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	36.35

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	-1000
Maximum Defocus (nm)	-1750
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	92000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	Data were collected by stage shifting to targeted exposure positions.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.0.6
IMAGE ACQUISITION	EPU	2.1
CTF CORRECTION	Gctf	1.06
MODEL FITTING	NAMD
MODEL FITTING	Coot
MODEL FITTING	UCSF Chimera
FINAL EULER ASSIGNMENT	RELION	3.0.6
CLASSIFICATION	RELION	3.0.6
RECONSTRUCTION	RELION	3.0.6
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Particles were CTF corrected during projection matching and back projection.	3500000	Particles were picked using Laplacian Gaussian auto-picking.