4LJ3

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++

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	2012-05-11
Detector	DECTRIS PILATUS 2M-F
Wavelength(s)	1.0000
Spacegroup name	P 1 21 1
Unit cell lengths	56.693, 70.300, 66.636
Unit cell angles	90.00, 98.68, 90.00

Refinement procedure

Resolution	20.630 - 1.700
R-factor	0.2228
Rwork	0.221
R-free	0.25430
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4kie
RMSD bond length	0.010
RMSD bond angle	1.510
Data reduction software	MOSFLM
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]	20.630	20.630	1.790
High resolution limit [Å]	1.700	5.380	1.700
Rmerge	0.093	0.070	0.370
Total number of observations		7368	29781
Number of reflections	56878
<I/σ(I)>	5.4426	5.96	1.78
Completeness [%]	99.8	98.17	99.97
Redundancy	3.42	4.02	3.59

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 alcohol mixture (200 mM of each of 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol and 1,3-propanediol), 100 mM MES/Imidazole pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K