5O4U
The flagellin of Pyrococcus furiosus
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5TFY |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.17 |
f_angle_d | 1.168 |
f_chiral_restr | 0.078 |
f_bond_d | 0.007 |
f_plane_restr | 0.007 |
Sample |
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archaellum |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details | blotting for 7-10 seconds |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | 13965 |
Reported Resolution (Å) | 4.2 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 5.5 |
Angular Rotation | 108 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5TFY) | ||||
Refinement Space | |||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 60 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | JEOL 3200FSC |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 3000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 4.2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | JEOL 3200FSC CRYOHOLDER |
Nominal Magnification | 30000 |
Calibrated Magnification | 44642 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | EMAN | |
PARTICLE SELECTION | RELION | 2.0 |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | Coot | 0.8.6 |
CLASSIFICATION | RELION | 2.0 |
RECONSTRUCTION | RELION | 2.0 |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | 74823 |