8BDX
Ternary complex between VCB, BRD4-BD2 and PROTAC 48
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SLS BEAMLINE X10SA |
Synchrotron site | SLS |
Beamline | X10SA |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-02-04 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.0000 |
Spacegroup name | P 32 |
Unit cell lengths | 82.341, 82.341, 168.960 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 71.310 - 2.930 |
R-factor | 0.1891 |
Rwork | 0.185 |
R-free | 0.25780 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5t35 |
RMSD bond length | 0.006 |
RMSD bond angle | 1.300 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0352) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 71.310 | 71.309 | 3.060 |
High resolution limit [Å] | 2.928 | 8.170 | 2.928 |
Rmerge | 0.069 | 0.025 | 1.386 |
Rmeas | 0.077 | 0.028 | 1.549 |
Rpim | 0.033 | 0.012 | 0.689 |
Total number of observations | 6472 | 6373 | |
Number of reflections | 25269 | 1263 | 1264 |
<I/σ(I)> | 14.3 | 44.9 | 1.2 |
Completeness [%] | 93.5 | 100 | 43.9 |
Redundancy | 5.3 | 5.1 | 5 |
CC(1/2) | 0.999 | 0.999 | 0.455 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 20% PEG 3350, 0.02M sodium/potassium phosphate, 0.1M bis-Tris propane pH 7.5 |