8TL6
Cryo-EM structure of DDB1deltaB-DDA1-DCAF5
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6Q0R | |
in silico model | RoseTTAFold |
Refinement
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.4492 |
f_angle_d | 0.4723 |
f_chiral_restr | 0.0455 |
f_plane_restr | 0.0037 |
f_bond_d | 0.0023 |
Sample |
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Complex of DDB1deltaB-DDA1-DCAF5 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | NITROGEN |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 547805 |
Reported Resolution (Å) | 2.63 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6q0r, 6q0r) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | 97 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 53.349 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TALOS ARCTICA |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 2500 |
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 | 36000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | Topaz | 0.2.4 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | cryoSPARC | v3.2 |
MODEL FITTING | UCSF ChimeraX | 1.4 |
MODEL FITTING | Coot | 0.9 |
INITIAL EULER ASSIGNMENT | cryoSPARC | v3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | v3.2 |
CLASSIFICATION | cryoSPARC | v3.2 |
RECONSTRUCTION | cryoSPARC | v4.1.2 |
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 | implemented in cryoSPARCv3.2 | 1404938 |