4LYK

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SLS BEAMLINE X06DA
Synchrotron site	SLS
Beamline	X06DA
Temperature [K]	100
Detector technology	PIXEL
Collection date	2012-09-03
Detector	DECTRIS PILATUS 2M
Wavelength(s)	1.0000
Spacegroup name	P 1 21 1
Unit cell lengths	64.850, 109.547, 81.750
Unit cell angles	90.00, 99.39, 90.00

Refinement procedure

Resolution	30.000 - 2.400
R-factor	0.1902
Rwork	0.189
R-free	0.22200
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4kie
RMSD bond length	0.013
RMSD bond angle	1.423
Data reduction software	XDS
Data scaling software	SCALA (CCP4_3.3.20)
Phasing software	PHASER
Refinement software	REFMAC (5.7.0029)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	109.550	109.550	2.530
High resolution limit [Å]	2.400	7.590	2.400
Rmerge	0.053	0.020	0.450
Total number of observations		4961	21003
Number of reflections	43912
<I/σ(I)>	14.5822	34.48	1.76
Completeness [%]	99.6	99	99.79
Redundancy	3.4	3.45	3.31

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 10 % of amino acid mixture (200 mM of each of Sodium-L-glutamate, M DL-alanine, Glycin and L-Lysine HCl, 0.2 M DL-Serin), 100 mM MES/Imidazole pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K