6H52
Crystal structure of human KDM5B in complex with compound 34g
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 | 142.120, 142.120, 152.400 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 31.330 - 2.140 |
| R-factor | 0.186 |
| Rwork | 0.185 |
| R-free | 0.20300 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5a1f |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.030 |
| 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] | 51.970 | 2.200 |
| High resolution limit [Å] | 2.140 | 2.140 |
| Rmerge | 0.080 | 1.455 |
| Number of reflections | 50252 | 3516 |
| <I/σ(I)> | 20.4 | 1.1 |
| Completeness [%] | 99.5 | 96.5 |
| Redundancy | 16.1 | 7.2 |
| CC(1/2) | 0.999 | 0.436 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION | 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 |
