6H50
Crystal structure of human KDM5B in complex with compound 34a
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I03 |
| Synchrotron site | Diamond |
| Beamline | I03 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-09-22 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.9763 |
| Spacegroup name | P 65 2 2 |
| Unit cell lengths | 142.360, 142.360, 152.780 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 32.060 - 2.190 |
| R-factor | 0.183 |
| Rwork | 0.182 |
| R-free | 0.20600 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5a1f |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.040 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.10.3) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 47.970 | 2.250 |
| High resolution limit [Å] | 2.190 | 2.190 |
| Rmerge | 0.114 | 1.284 |
| Number of reflections | 47457 | 3450 |
| <I/σ(I)> | 18.3 | 1.4 |
| Completeness [%] | 99.9 | 99.9 |
| Redundancy | 16.8 | 8.3 |
| CC(1/2) | 0.999 | 0.494 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 100 nL of protein is mixed with 200 nL of crystallisation solution containing 1.6 M Na/K phosphate, 0.1 M HEPES pH 7.5, and with 20 nL of seeds obtained in the same conditions. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound |
