8I9Q
The focused refinement of CCT4-PhLP2A from TRiC-PhLP2A complex in the open state
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6NR8 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.992 |
f_angle_d | 0.803 |
f_chiral_restr | 0.049 |
f_plane_restr | 0.006 |
f_bond_d | 0.005 |
Sample |
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Complex of human TRiC/CCT-PhLP2A |
Sample Components |
T-complex protein 1 subunit delta from human TRiC/CCT complex |
PhLP2A (PDCL3) |
Specimen Preparation | |
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Sample Aggregation State | 2D ARRAY |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
---|---|
Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 485964 |
Reported Resolution (Å) | 4.22 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6NR8) | ||||
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 IV (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2000 |
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 | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 3.2.0 |
CTF CORRECTION | cryoSPARC | 3.2.0 |
MODEL FITTING | UCSF Chimera | 1.15 |
MODEL REFINEMENT | PHENIX | 1.19 |
MODEL REFINEMENT | Coot | 0.9.6 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
CLASSIFICATION | cryoSPARC | 3.2.0 |
RECONSTRUCTION | cryoSPARC | 3.2.0 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE | CTF correction was performed for every micrographs | 2691733 | The initial particle selection after 2D class classification |