6IUG | pdb_00006iug

Cryo-EM structure of the plant actin filaments from Zea mays pollen

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OOC

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.081
f_angle_d	0.892
f_chiral_restr	0.055
f_plane_restr	0.007
f_bond_d	0.005

Sample
The actin filament from Zea mays pollen

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blotting time of 5.5 s and blotting force of level 2

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	35684
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	27.5
Angular Rotation	-166.77

Map-Model Fitting and Refinement
Id	1 (5OOC)
Refinement Space	RECIPROCAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Correlation coefficient
Overall B Value	70
Fitting Procedure
Details	Chain C from pdb 5OOC was rigid body fitted to plant actin map using Chimera; Then Phenix was used for real space refinement. Finally, filament with 5 real space refinement units were generated using helical parameter, and this filament with 5 units was real space refined using Phenix again.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	39

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	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	22500
Calibrated Magnification	22013
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	SPIDER	24.08
IMAGE ACQUISITION	SerialEM	3.5
CTF CORRECTION	Gctf	1.18
MODEL FITTING	UCSF Chimera	1.10.1
MODEL FITTING	Coot	7.0
MODEL REFINEMENT	PHENIX	1.11.1
INITIAL EULER ASSIGNMENT	SPIDER	24.08
FINAL EULER ASSIGNMENT	SPIDER	24.08
CLASSIFICATION	SPIDER	24.08
RECONSTRUCTION	SPIDER	24.08

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		40943	A total of 8,609 ZMPA filaments were boxed using e2helixboxer.py in the package of EMAN2 with box width 168 and 77% box-overlap. A total of 40,943 segments were generated with box-size of 384.