8A2Y | pdb_00008a2y

Cryo-EM structure of F-actin in the Ca2+-ADP-Pi nucleotide state.

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AHN

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.8975
f_angle_d	0.579
f_chiral_restr	0.0461
f_bond_d	0.004
f_plane_restr	0.004

Sample
rabbit skeletal alpha-actin in the filamentous state.

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	The Vitrobot was operated at 13 degrees celsius and the samples were blotted for 9 seconds with a blot force of -25.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	2171987
Reported Resolution (Å)	2.15
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7AHN)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	The structures were then refined through a similar protocol of iterative cycles in Coot and phenix real-space refine. All solvent molecules (ions, waters) were placed manually in Coot in the central actin subunit, and were then placed in the other subunits using NCS. Because the local resolution of each F-actin reconstruction is highest in the center and lower at the periphery of the map, we inspected all waters in each structure manually before the final phenix refinement; water molecular with poor corresponding cryo-EM density were removed.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	88.8

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2000
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.8
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.13
MODEL FITTING	UCSF ChimeraX	1.3
MODEL REFINEMENT	PHENIX	v1.20.1-4487
INITIAL EULER ASSIGNMENT	SPHIRE	1.4
FINAL EULER ASSIGNMENT	RELION	3.1.0
CLASSIFICATION	RELION	3.1.0
RECONSTRUCTION	RELION	3.1.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3031270	We picked helical segments with a box distance of 40 pixels or 27.8 Angstrom and a minimum number of six boxes per filament.