6H51
Crystal structure of human KDM5B in complex with compound 34f
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 | 142.000, 142.000, 152.410 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 32.360 - 2.210 |
R-factor | 0.183 |
Rwork | 0.182 |
R-free | 0.19700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5a1f |
RMSD bond length | 0.010 |
RMSD bond angle | 1.050 |
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] | 51.950 | 2.270 |
High resolution limit [Å] | 2.210 | 2.210 |
Rmerge | 0.094 | 1.491 |
Number of reflections | 45895 | 3334 |
<I/σ(I)> | 18.7 | 1.3 |
Completeness [%] | 99.9 | 100 |
Redundancy | 17.1 | 8.9 |
CC(1/2) | 0.999 | 0.460 |
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 |