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.