5YX1

Crystal structure of hematopoietic prostaglandin D synthase in complex with U004

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL41XU
Synchrotron site	SPring-8
Beamline	BL41XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2016-11-22
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1.0
Spacegroup name	P 1
Unit cell lengths	48.447, 47.119, 91.924
Unit cell angles	92.20, 98.67, 90.00

Refinement procedure

Resolution	47.940 - 1.390
R-factor	0.1863
Rwork	0.185
R-free	0.21590
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2cvd
RMSD bond length	0.010
RMSD bond angle	1.566
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	MOLREP (11.0.05)
Refinement software	REFMAC (5.7.0029)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	70.000	70.000	1.400
High resolution limit [Å]	1.390	4.750	1.390
Rmerge	0.096	0.053	0.570
Number of reflections	144547	3761	3435
<I/σ(I)>	6.7
Completeness [%]	89.3	93.2	86.5
Redundancy	3.1	3.4	2.8

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	LIQUID DIFFUSION	8.5	293	35% PEG 6000, 5 mM DTT, 2 mM MgCl2, 2 mM Glutathione, 2% Dioxane, 50 mM Tris-HCl, pH 8.5