7RWA
AP2 bound to heparin and Tgn38 tyrosine cargo peptide
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VGL |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.155 |
f_angle_d | 0.888 |
f_chiral_restr | 0.047 |
f_bond_d | 0.003 |
f_plane_restr | 0.003 |
Sample |
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AP2 bound to heparin and Tgn38 tyrosine cargo peptide |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details | Blot force -10, 4 second blot, 4 uL sample |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 372971 |
Reported Resolution (Å) | 4.7 |
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 (2VGL) | ||||
Refinement Space | |||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | phenix.real_space_refine |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 55 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TALOS ARCTICA |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 36000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 3.1.1 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | cryoSPARC | 3.2.0 |
MODEL FITTING | Coot | 0.8.9.1 |
MODEL FITTING | UCSF Chimera | 1.14 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
RECONSTRUCTION | cryoSPARC | 3.2.0 |
MODEL REFINEMENT | PHENIX | 1.19.2 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |