6F6J

Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 1
Synchrotron site	SOLEIL
Beamline	PROXIMA 1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2015-04-14
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97857
Spacegroup name	P 1
Unit cell lengths	56.950, 67.390, 110.650
Unit cell angles	107.55, 102.87, 93.58

Refinement procedure

Resolution	40.000 - 2.000
R-factor	0.196
Rwork	0.194
R-free	0.22500
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.020
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MOLREP
Refinement software	BUSTER (2.10.3)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.050
High resolution limit [Å]	2.000	2.000
Rmeas	0.008	0.833
Number of reflections	101680	7144
<I/σ(I)>	13.63	1.38
Completeness [%]	99.0	93.1
Redundancy	5.85	2.985
CC(1/2)	0.998	0.738

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	KDO1: 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05 M Tris-HCl, pH 8 Precipitant: 18% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate. Soaking/cryo : 20% PEG3350, 0.15 M Tris pH 7.5, 0.2 M NaCl, 0.02 M Na Succinate, 0.001 M FeIISO4 (0.5 M stock solution prepared in 0.050 M dithionite), 0.05 M alpha-KG, 0.05 M L-Lysine, 20% glycerol