7T5Q | pdb_00007t5q

Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JD2

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.043
f_angle_d	0.834
f_chiral_restr	0.049
f_plane_restr	0.006
f_bond_d	0.005

Sample
bovine Arp2/3 complex and Actin, CapZ
Sample Components
bovine Arp2/3
Actin skeletal muscle
F-actin-capping protein

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM CPC
Cryogen Name	ETHANE
Sample Vitrification Details	Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	269760
Reported Resolution (Å)	3.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Composite map after multibody refinement
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4JD2)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	correlation
Overall B Value	132
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	3500
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	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Data were collected in super-resolution mode with an illuminated area of 1.01 um, nominal dose of 40 e-/A^2, a dose rate of 4.87 e-/s/pixel, and 2 or 5 exposures per hole by image shift.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	2.12.4
IMAGE ACQUISITION	Latitude
CTF CORRECTION	CTFFIND	4.1.13
CTF CORRECTION	cryoSPARC	2.12.4
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	RELION	3.1
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	cryoSPARC	4.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF correction was done in cryoSPARC for intial 2D classification and then repeated in CTFFIND4 (Relion) for classification and final reconstruction.	4485066	Particles autopicked in cryoSPARC