6IBF

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417

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	2018-03-11
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.91587
Spacegroup name	P 21 21 21
Unit cell lengths	98.476, 110.511, 160.298
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	80.110 - 2.310
R-factor	0.20621
Rwork	0.203
R-free	0.26234
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.008
RMSD bond angle	1.560
Data reduction software	DIALS
Data scaling software	Aimless
Phasing software	REFMAC
Refinement software	REFMAC (5.8.0238)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	80.110	2.370
High resolution limit [Å]	2.310	2.310
Rmerge	0.124	0.741
Rmeas	0.135	0.803
Rpim	0.053	0.307
Number of reflections	77377	5650
<I/σ(I)>	8.3	2
Completeness [%]	100.0	100
Redundancy	6.5	6.7
CC(1/2)	0.994	0.584

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES pH 7.5