4OEC

Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL44XU
Synchrotron site	SPring-8
Beamline	BL44XU
Temperature [K]	100
Detector technology	CCD
Collection date	2012-07-04
Detector	BRUKER SMART 6500
Wavelength(s)	0.9
Spacegroup name	P 21 21 21
Unit cell lengths	43.724, 132.034, 171.639
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	50.000 - 1.900
R-factor	0.197
Rwork	0.194
R-free	0.24990
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2otd
RMSD bond length	0.008
RMSD bond angle	0.978
Data reduction software	DENZO
Data scaling software	SCALEPACK
Phasing software	MOLREP
Refinement software	REFMAC (5.5.0109)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.930
High resolution limit [Å]	1.900	5.160	1.900
Rmerge	0.142	0.095	0.558
Number of reflections	79998
<I/σ(I)>	23.493
Completeness [%]	99.8	99.2	100
Redundancy	13.6	13	14.4

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	30%(w/v) PEG4000, 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K