6RWK
MxiD N0 N1 and MxiG C-terminal domains of the Shigella type 3 secretion system
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GR5 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.157 |
f_angle_d | 0.744 |
f_chiral_restr | 0.046 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Sample |
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Oligomer of the secretin N0 and N1 domains in complex with the inner membrane ring of the Shigella type 3 secretion system |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Dra ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 72298 |
Reported Resolution (Å) | 3.86 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C8 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (3GR5) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | AB INITIO MODEL | ||||
Refinement Target | Correlation coefficient and geometry | ||||
Overall B Value | 120 | ||||
Fitting Procedure | |||||
Details | Model was built and refined in the map low-pass filtered at 3.5 A |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON II (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 25 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1.5 |
Maximum Defocus (nm) | 4 |
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 | 101179 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 1.4 |
CTF CORRECTION | CTFFIND | 3.5 |
MODEL FITTING | UCSF Chimera | 1.13.1 |
INITIAL EULER ASSIGNMENT | RELION | 2.1 |
FINAL EULER ASSIGNMENT | RELION | 2.1 |
CLASSIFICATION | RELION | 2.1 |
RECONSTRUCTION | RELION | 2.1 |
MODEL REFINEMENT | PHENIX | 3357 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 171833 |