6ZBA

Crystal structure of PDE4D2 in complex with inhibitor LEO39652

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04-1
Synchrotron site	Diamond
Beamline	I04-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-09-23
Detector	DECTRIS EIGER2 X 9M
Wavelength(s)	0.9159
Spacegroup name	P 21 21 21
Unit cell lengths	100.030, 111.866, 159.623
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	79.939 - 1.600
Rwork	0.162
R-free	0.19180
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1y2k
RMSD bond length	0.010
RMSD bond angle	1.590
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	REFMAC
Refinement software	REFMAC (5.8.0258)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	79.939	1.630
High resolution limit [Å]	1.600	1.600
Rmerge	0.085	1.481
Number of reflections	235229	11558
<I/σ(I)>	9.2	1
Completeness [%]	100.0	100
Redundancy	6.6	6
CC(1/2)	0.997	0.422

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	Protein stored at 20.6 mg/mL in a storage buffer of 50 mM NaCl, 20 mM Tris HCl (pH 7.5), 1 mM TCEP, 1 mM EDTA. Reservoir was 0.1 M HEPES (pH 7.5), 19% PEG3350, 25% ethylene glycol, 5% 2-propanol, 5% glycerol. Drops were microseeded. Apo crystals were soaked with 0.8 mM LEO39652A for 3 days.