8OJH
Crystal structure of human CRBN-DDB1 in complex with compound 4
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I24 |
| Synchrotron site | Diamond |
| Beamline | I24 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-12-04 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.9999 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 72.016, 128.595, 198.454 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 49.610 - 2.720 |
| R-factor | 0.211 |
| Rwork | 0.209 |
| R-free | 0.25410 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.920 |
| Data reduction software | DIALS |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.10.4 (21-NOV-2022)) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 49.610 | 49.610 | 2.810 |
| High resolution limit [Å] | 2.720 | 10.880 | 2.720 |
| Rmerge | 0.289 | 0.127 | 2.640 |
| Rmeas | 0.301 | 0.134 | 2.754 |
| Rpim | 0.085 | 0.041 | 0.779 |
| Total number of observations | 626437 | 9761 | 56365 |
| Number of reflections | 50451 | 905 | 4552 |
| <I/σ(I)> | 6.6 | 17.3 | 1 |
| Completeness [%] | 100.0 | 99 | 100 |
| Redundancy | 12.4 | 10.8 | 12.4 |
| CC(1/2) | 0.988 | 0.981 | 0.429 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.2 | 291 | 0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution. |
