7AML
RET/GDNF/GFRa1 extracellular complex Cryo-EM structure
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 23.629 |
f_angle_d | 0.819 |
f_chiral_restr | 0.057 |
f_bond_d | 0.005 |
f_plane_restr | 0.004 |
Sample |
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Ternary complex of RET extracellular domain with GDNF and GFRa1 ligand-coreceptor pair |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK II |
Cryogen Name | ETHANE |
Sample Vitrification Details | 90 s wait time, 5 s blot time |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 382547 |
Reported Resolution (Å) | 3.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (7AB8) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
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) | 48.6 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1400 |
Maximum Defocus (nm) | 3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 46296 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | |
PARTICLE SELECTION | Gautomatch | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.1 |
MODEL FITTING | PHENIX | 1.18.2 |
INITIAL EULER ASSIGNMENT | RELION | |
FINAL EULER ASSIGNMENT | cryoSPARC | 2 |
CLASSIFICATION | cryoSPARC | 2 |
RECONSTRUCTION | cryoSPARC | 2 |
MODEL REFINEMENT | PHENIX | 1.18.2 |
MODEL REFINEMENT | Coot |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 2549540 | 1156517 particles picked from 0 tilt data, 1393023 particles picked from 30-degree tilt data |