6ZRB
Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | MAX IV BEAMLINE BioMAX |
Synchrotron site | MAX IV |
Beamline | BioMAX |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-04-11 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.918 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 60.935, 65.989, 107.318 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 56.280 - 1.550 |
R-factor | 0.1664 |
Rwork | 0.165 |
R-free | 0.18450 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6Z2R |
RMSD bond length | 0.007 |
RMSD bond angle | 1.517 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 107.320 | 1.580 |
High resolution limit [Å] | 1.550 | 1.550 |
Rmerge | 0.052 | 0.450 |
Rmeas | 0.057 | 0.532 |
Rpim | 0.025 | 0.277 |
Number of reflections | 62691 | 2667 |
<I/σ(I)> | 16.4 | 2.3 |
Completeness [%] | 98.7 | 86.6 |
Redundancy | 5 | 3.3 |
CC(1/2) | 0.999 | 0.789 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.25 | 298 | Protein was pre-incubated with the covalent inhibitor, 7 mg/mL and 0.4 mM, respectively, for 8 h at RT. Crystallization was performed in 2 uL hanging drops, 1:1 protein to reservoir ratio, reservoir: 16% PEG3350, 100 mM Tris (pH 8.25), 100 mM Mg(OAc)2). Protein crystals were cryoprotected in 20% PEG3350, 100 mM Tris (pH 8.25), 100 mM Mg(OAc)2, 10% DMSO and 10% glycerol. |