3Q4D

Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2010-06-03
Detector	RAYONIX MX-225
Wavelength(s)	0.97872
Spacegroup name	P 1 21 1
Unit cell lengths	94.560, 158.090, 182.180
Unit cell angles	90.00, 100.04, 90.00

Refinement procedure

Resolution	20.000 - 3.000
R-factor	0.23106
Rwork	0.230
R-free	0.25388
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1tkk
RMSD bond length	0.009
RMSD bond angle	1.009
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	REFMAC (5.5.0109)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	20.000	20.000	3.110
High resolution limit [Å]	3.000	6.400	3.000
Rmerge	0.138	0.030	0.716
Number of reflections	105392
<I/σ(I)>	11.88	26.93	2.4
Completeness [%]	99.8	98.9	100
Redundancy	10.3

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	4	277	Precipitant contained 10% PEG 4000 and 0.1M Na-citrate. Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Ala, Protein concentration was 40 mg/mL, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K