6YAF
AP2 on a membrane containing tyrosine-based cargo peptide
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XA7 |
Sample |
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AP2 on membranes |
Sample Components |
AP-2 complex subunits alpha-2 and mu |
AP-2 complex subunit beta |
AP-2 complex subunit sigma |
Tyrosine type cargo signal derived from TGN38 |
Specimen Preparation | |
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Sample Aggregation State | 3D ARRAY |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details | The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds. |
3D Reconstruction | |
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Reconstruction Method | SUBTOMOGRAM AVERAGING |
Number of Particles | 100556 |
Reported Resolution (Å) | 9.1 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (2XA7) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 3.2 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 6500 |
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 |
EM Software | ||
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Task | Software Package | Version |
VOLUME SELECTION | TOM | |
IMAGE ACQUISITION | SerialEM | 3.6 |
CTF CORRECTION | NOVACTF | 1.0 |
MODEL FITTING | MDFF | 1.7 |
FINAL EULER ASSIGNMENT | TOM | |
FINAL EULER ASSIGNMENT | AV3 | |
RECONSTRUCTION | TOM | |
RECONSTRUCTION | AV3 | |
MODEL REFINEMENT | PHENIX |
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 correction in novaCTF with by multiplication |