6EMK
Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FVM |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 47.64 |
r_dihedral_angle_2_deg | 40.828 |
r_dihedral_angle_3_deg | 23.376 |
r_mcangle_it | 19.394 |
r_dihedral_angle_4_deg | 16.619 |
r_scbond_it | 11.153 |
r_dihedral_angle_1_deg | 10.876 |
r_mcbond_it | 10.668 |
r_angle_refined_deg | 2.024 |
r_chiral_restr | 0.153 |
Sample |
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Target of rapamycin protein complex 2 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 2 - 3 sec blotting |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 16190 |
Reported Resolution (Å) | 7.9 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Number of Particles | 10663 |
Reported Resolution (Å) | 8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (5FVM) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON II (4k x 4k) | GATAN K2 QUANTUM (4k x 4k) | |||||||
Electron Dose (electrons/Å**2) | 50 | 47 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 3500 |
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 | 105000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | SerialEM | 3.6 |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | Coot | 0.8.8 |
INITIAL EULER ASSIGNMENT | RELION | 1.4 |
FINAL EULER ASSIGNMENT | RELION | 1.4 |
RECONSTRUCTION | RELION | 1.4 |
PARTICLE SELECTION | EMAN2 | |
CTF CORRECTION | CTFFIND | 4 |
INITIAL EULER ASSIGNMENT | RELION | 1.4 |
FINAL EULER ASSIGNMENT | RELION | 1.4 |
RECONSTRUCTION | RELION | 1.4 |
MODEL REFINEMENT | REFMAC | 5.8.0158 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 350000 | |||
PHASE FLIPPING AND AMPLITUDE CORRECTION | 200000 |