5D6Y

Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2014-10-23
Detector	MARMOSAIC 225 mm CCD
Wavelength(s)	0.979
Spacegroup name	P 32
Unit cell lengths	106.159, 106.159, 79.206
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	28.581 - 2.287
R-factor	0.265
Rwork	0.264
R-free	0.29470
RMSD bond length	0.011
RMSD bond angle	1.391
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHENIX
Refinement software	PHENIX

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000		2.420
High resolution limit [Å]	2.287	6.690	2.290
Rmerge	0.217	0.044	1.752
Rmeas	0.239	0.049	1.970
Total number of observations	466605
Number of reflections	82623	3546	14423
<I/σ(I)>	9.15	29.15	1.12
Completeness [%]	91.5	98.8	99.6
Redundancy	5.68

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol