7AQK | pdb_00007aqk

Model of the actin filament Arp2/3 complex branch junction in cells

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TYQ
experimental model	PDB	4JD2
experimental model	PDB	1K8K
experimental model	PDB	6T20

Sample
Actin Filament Arp2/3 Complex Branch Junction

Specimen Preparation
Sample Aggregation State	CELL
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducial ...	Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	14296
Reported Resolution (Å)	9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 1TYQ, 4JD2, 4JD2, 1K8K, 6T20, 6T20, 6T20, 6T20, 6T20)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	2.79

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	-1.75
Maximum Defocus (nm)	-5.5
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	42000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
VOLUME SELECTION	Dynamo	1.133
VOLUME SELECTION	Warp	1.07
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Warp	1.07
MODEL FITTING	UCSF Chimera	1.13.1
FINAL EULER ASSIGNMENT	RELION	3.0.9
CLASSIFICATION	RELION	3.0.9
RECONSTRUCTION	RELION	3.0.9
MODEL REFINEMENT	ISOLDE	1.0b5
MODEL REFINEMENT	Coot	0.8.9.3

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.