8G3E
Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17U1 |
Synchrotron site | SSRF |
Beamline | BL17U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-08-30 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.000 |
Spacegroup name | P 1 |
Unit cell lengths | 46.662, 62.276, 64.381 |
Unit cell angles | 114.09, 91.08, 110.17 |
Refinement procedure
Resolution | 32.350 - 1.330 |
R-factor | 0.14066 |
Rwork | 0.139 |
R-free | 0.17047 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8f1g |
RMSD bond length | 0.006 |
RMSD bond angle | 1.323 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MOLREP |
Refinement software | REFMAC (v5.8.0253) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 32.350 | 1.363 |
High resolution limit [Å] | 1.330 | 1.330 |
Rmerge | 0.063 | 1.000 |
Number of reflections | 133465 | 8976 |
<I/σ(I)> | 7.15 | |
Completeness [%] | 88.9 | |
Redundancy | 2.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 23.5% PEG3350, 0.21 M ammonium sulfate, 0.1 M HEPES, pH 7.5 |