7UX3
Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 7.6832 |
f_angle_d | 0.2409 |
f_chiral_restr | 0.0864 |
f_plane_restr | 0.0008 |
f_bond_d | 0.0007 |
Sample |
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Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulated lipid bilayer |
Sample Components |
AP-1 heterotetramer |
Arf1, Nef and MHC-I cytosolic tail |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was do ... |
3D Reconstruction | |
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Reconstruction Method | SUBTOMOGRAM AVERAGING |
Number of Particles | 16422 |
Reported Resolution (Å) | 9.6 |
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 (6CM9, 4EN2, 4EN2) | ||||
Refinement Space | |||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 3 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 4500 |
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 | 42000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
VOLUME SELECTION | Dynamo | 1.1.532 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | NOVACTF | |
MODEL FITTING | UCSF Chimera | 1.14 |
MODEL FITTING | UCSF ChimeraX | 1.3 |
RECONSTRUCTION | RELION | 3.1.1 |
MODEL REFINEMENT | PHENIX | 1.20-4459 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | CTF was estimated on a per-tilt basis in IMOD (4.11) using CTFPLOTTER. The results were used as input to NOVACTF during 3DCTF correction. |