8G46
Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.362 |
r_long_range_B_other | 16.581 |
r_long_range_B_refined | 16.577 |
r_scangle_other | 10.079 |
r_mcangle_it | 9.391 |
r_mcangle_other | 9.391 |
r_scbond_it | 6.489 |
r_scbond_other | 6.488 |
r_mcbond_it | 6.389 |
r_mcbond_other | 6.387 |
Sample |
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Ternary complex of cullin ring E3 ubiquitin ligase substrate receptor arm (DDB1deltaB-DDA1-DCAF16) in compound-induced complex with bromodomain 2 of BRD4 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details | detergent added directly before grid application |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 1433050 |
Reported Resolution (Å) | 2.2 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6VIX, 6Q0R) | ||||
Refinement Space | |||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | 74 | ||||
Fitting Procedure | |||||
Details | refinement in both real and Fourier space |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50.27 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
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 | 105000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | Topaz | |
IMAGE ACQUISITION | SerialEM | 4.0.5 |
CTF CORRECTION | cryoSPARC | 3.3.2 |
MODEL FITTING | UCSF ChimeraX | 1.4 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
CLASSIFICATION | cryoSPARC | 3.3.2 |
RECONSTRUCTION | cryoSPARC | 3.3.2 |
MODEL REFINEMENT | ISOLDE | 1.3 |
MODEL REFINEMENT | REFMAC | 5.8 |
MODEL REFINEMENT | PHENIX | 1.19 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | in cryoSPARC | 14452363 |