5FZK
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment N,3-dimethyl-N-(pyridin-3-ylmethyl)-1,2-oxazole-5- carboxamide (N10051a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
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 | 2015-05-19 |
Detector | DECTRIS PILATUS 2M |
Spacegroup name | P 65 2 2 |
Unit cell lengths | 142.050, 142.050, 152.130 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 71.025 - 2.050 |
R-factor | 0.2054 |
Rwork | 0.204 |
R-free | 0.23820 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5a3p |
RMSD bond length | 0.009 |
RMSD bond angle | 1.161 |
Data reduction software | XDS |
Data scaling software | SCALA |
Phasing software | DIMPLE |
Refinement software | PHENIX ((PHENIX.REFINE)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 76.070 | 2.100 |
High resolution limit [Å] | 2.050 | 2.050 |
Rmerge | 0.180 | 1.500 |
Number of reflections | 57203 | |
<I/σ(I)> | 11.6 | 1.4 |
Completeness [%] | 100.0 | 100 |
Redundancy | 19.3 | 20.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | 7.5 | 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC |