6NYY
human m-AAA protease AFG3L2, substrate-bound
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6AZ0 |
Sample |
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AFG3L2 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details | Sample was blotted for 3 seconds using Whatman No. 1 filter paper immediately prio to plunge-freezing. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 1129437 |
Reported Resolution (Å) | 3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Multi-body refinement was used to generate 3 different reconstructions that were stitched together |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6AZ0) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | 85 | ||||
Fitting Procedure | |||||
Details | The sequence was threaded onto the PDB ID 6AZ0 and built into the EM density with Coot. |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI ARCTICA |
Minimum Defocus (nm) | 8000 |
Maximum Defocus (nm) | 18000 |
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 | 36000 |
Calibrated Magnification | 43478 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | FindEM | |
IMAGE ACQUISITION | Leginon | 3.2 |
CTF CORRECTION | CTFFIND | 4 |
CTF CORRECTION | RELION | 3.0 |
MODEL FITTING | UCSF Chimera | 1.11.2 |
INITIAL EULER ASSIGNMENT | RELION | 3.0 |
FINAL EULER ASSIGNMENT | RELION | 3.0 |
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | PHENIX | 1.11.1_2580 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF estimated with CTFFIND 4, local CTF estimated with | 4541491 | Picked with FindEM |