8G3C
Crystal structure of human WDR5 in complex with N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide (compound 1, WDR5-MYC PPI 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 | CCD |
Collection date | 2018-03-12 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.97919 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 48.815, 56.203, 118.429 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 40.760 - 1.800 |
R-factor | 0.20511 |
Rwork | 0.204 |
R-free | 0.22407 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8f1g |
RMSD bond length | 0.007 |
RMSD bond angle | 1.199 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | REFMAC (v5.8.0218) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.840 |
High resolution limit [Å] | 1.800 | 1.800 |
Rmerge | 0.157 | 1.003 |
Number of reflections | 30595 | 2152 |
<I/σ(I)> | 11.9 | |
Completeness [%] | 98.8 | |
Redundancy | 12.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 20% PEG3350, 0.2 M potassium acetate |