7K21 | pdb_00007k21

Cryo-EM structure of pyrene-labeled ADP-Pi-actin filaments

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DJN

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.599
f_angle_d	0.788
f_chiral_restr	0.056
f_bond_d	0.007
f_plane_restr	0.007

Sample
Pyrene-labeled ADP-Pi-actin filaments

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	462669
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	27.369141
Angular Rotation	-166.57062

Map-Model Fitting and Refinement
Id	1 (6DJN)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Restraints for pyrene were generated with eLBOW in Phenix. The coordinates of actin and pyrene were joined together manually in a text editor, and then fitted into the map in Coot.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	67.9

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	Gctf	1.18
MODEL FITTING	Coot	1.3.0
RECONSTRUCTION	RELION	3.08
MODEL REFINEMENT	PHENIX	3.12

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