6IUG
Cryo-EM structure of the plant actin filaments from Zea mays pollen
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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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 |
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The actin filament from Zea mays pollen |
Specimen Preparation | |
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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 | |
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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 | |||||
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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 ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 39 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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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. |