6H0F
Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SLS BEAMLINE X06DA |
Synchrotron site | SLS |
Beamline | X06DA |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-01-30 |
Detector | DECTRIS PILATUS 2M-F |
Wavelength(s) | 1.000 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 161.450, 177.860, 242.470 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 39.850 - 3.250 |
R-factor | 0.213 |
Rwork | 0.212 |
R-free | 0.23400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5fqd |
RMSD bond length | 0.015 |
RMSD bond angle | 0.970 |
Data reduction software | DIALS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | BUSTER (2.11.7) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 39.850 | 39.850 | 3.310 |
High resolution limit [Å] | 3.250 | 17.800 | 3.250 |
Rmerge | 0.345 | 0.060 | 2.743 |
Rmeas | 0.351 | 0.061 | 2.870 |
Rpim | 0.061 | 0.010 | 0.822 |
Number of reflections | 104192 | 700 | 2706 |
<I/σ(I)> | 11.5 | ||
Completeness [%] | 94.4 | 91.3 | 50.1 |
Redundancy | 31.3 | 34.3 | 11.3 |
CC(1/2) | 0.997 | 1.000 | 0.340 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 293 | Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether. |