9FJX
Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I04-1 |
| Synchrotron site | Diamond |
| Beamline | I04-1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-10-23 |
| Detector | DECTRIS EIGER2 XE 9M |
| Wavelength(s) | 0.9159 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 71.673, 129.068, 198.446 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 20.150 - 2.000 |
| R-factor | 0.1978 |
| Rwork | 0.196 |
| R-free | 0.23190 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.000 |
| Data reduction software | DIALS |
| Data scaling software | Aimless (0.5.32) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.10.4 (26-JUL-2023)) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 49.610 | 49.610 | 2.030 |
| High resolution limit [Å] | 2.000 | 10.950 | 2.000 |
| Rmerge | 0.114 | 0.032 | 2.123 |
| Rmeas | 0.123 | 0.034 | 2.324 |
| Rpim | 0.046 | 0.013 | 0.928 |
| Total number of observations | 900114 | 6304 | 38719 |
| Number of reflections | 124900 | 890 | 6121 |
| <I/σ(I)> | 9.7 | 38.4 | 0.9 |
| Completeness [%] | 99.9 | 99.1 | 99.9 |
| Redundancy | 7.2 | 7.1 | 6.3 |
| CC(1/2) | 0.998 | 0.999 | 0.309 |
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. |
