8S6H
Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 10.2606 |
f_angle_d | 0.3786 |
f_chiral_restr | 0.0349 |
f_bond_d | 0.0033 |
f_plane_restr | 0.0024 |
Sample |
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Conjugative pilus from the E. coli R388 plasmid |
Specimen Preparation | |
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Sample Aggregation State | HELICAL ARRAY |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | C-flat grids (Protochips, US 1.2/1.3 400 mesh) were negatively glow discharged using PELCO Easiglow (Ted Pella, USA) and coated with graphene oxide. 3 ... |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | 209930 |
Reported Resolution (Å) | 3.39 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Find more details in the Methods section of the publication |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 13.241 |
Angular Rotation | 28.983 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | |||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Cross-correlation in Phenix | ||||
Overall B Value | 109.7 | ||||
Fitting Procedure | |||||
Details | Find more details in the Methods section of the publication |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 34.67 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 900 |
Maximum Defocus (nm) | 2400 |
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 | 81000 |
Calibrated Magnification | 81000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | The R388 pilus data were collected at the ISMB Birkbeck EM facility using a Titan Krios microscope (Thermo Fisher Scientific, USA) operated at 300 keV and equipped with a BioQuantum energy filter (Gatan, USA) with a slit width of 20 eV. The images were collected with a post-GIF K3 direct electron detector (Gatan, USA) operating in super resolution mode, at a magnification of 81,000 corresponding to a pixel size of 1.067 A. The dose rate was set to 14.62 e per pixel per second and a total dose of 34.67 e per A2 was fractionated over 50 frames. |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | CRYOSPARC v4.3.1 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | CRYOSPARC v4.3.1 |
MODEL FITTING | Coot | COOT v0.9.3 |
INITIAL EULER ASSIGNMENT | cryoSPARC | CRYOSPARC v4.3.1 |
FINAL EULER ASSIGNMENT | cryoSPARC | CRYOSPARC v4.3.1 |
CLASSIFICATION | cryoSPARC | CRYOSPARC v4.3.1 |
RECONSTRUCTION | cryoSPARC | CRYOSPARC v4.3.1 |
MODEL REFINEMENT | PHENIX | 1.21rc1_5058 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Find more details in the Methods section of the publication | 1158759 | Find more details in the Methods section of the publication |