8QQM
nicotinic acetylcholine receptor in intact synaptic membrane
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7SMM |
Sample |
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Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane |
Specimen Preparation | |
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Sample Aggregation State | HELICAL ARRAY |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 107524 |
Reported Resolution (Å) | 4.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | The volumes for FSC determination were cut out from helical reconstructions of each class average |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (7SMM, 7SMM, 7SMM, 7SMM, 7SMM) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | 350 | ||||
Fitting Procedure | |||||
Details | Refinement parameters were chosen to minimise changes to the original secondary structure |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1200 |
Maximum Defocus (nm) | 2800 |
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 | 59000 |
Calibrated Magnification | 104478 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | All images taken manually: by searching at low magnification for long straight and narrow tubes, then recording in integrating mode |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 2.1 and 3.1 |
IMAGE ACQUISITION | DigitalMicrograph | |
CTF CORRECTION | Gctf | |
MODEL FITTING | DireX | |
CLASSIFICATION | RELION | 2.1 |
RECONSTRUCTION | RELION | 2.1 |
MODEL REFINEMENT | DireX | |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Correction performed by standard procedure in RELION | 160652 | 160652 tube segments from 4045 selected micrographs were reduced to 107524 tube segments after 2D classification |