8A2T

Cryo-EM structure of F-actin in the Mg2+-ADP nucleotide state.


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.6601
f_angle_d0.54
f_chiral_restr0.0434
f_plane_restr0.0037
f_bond_d0.0034
Sample
rabbit skeletal alpha-actin in the filamentous state.
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsThe Vitrobot was operated at 13 degrees celsius and the samples were blotted for 9 seconds with a blot force of -25.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1114051
Reported Resolution (Å)2.24
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7AHN)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe structures were then refined through a similar protocol of iterative cycles in Coot and phenix real-space refine. All solvent molecules (ions, wat ...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 TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)76.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO1.8
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.13
MODEL FITTINGUCSF ChimeraX1.3
INITIAL EULER ASSIGNMENTSPHIRE1.4
FINAL EULER ASSIGNMENTRELION3.1.0
CLASSIFICATIONRELION3.1.0
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIXv1.20.1-4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1296776We picked helical segments with a box distance of 40 pixels or 27.8 Angstrom and a minimum number of six boxes per filament.