4OAK

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	ROTATING ANODE
Source details	RIGAKU MICROMAX-007 HF
Temperature [K]	100
Detector technology	IMAGE PLATE
Collection date	2013-12-12
Detector	RIGAKU RAXIS IV++
Wavelength(s)	1.5418
Spacegroup name	P 1
Unit cell lengths	41.939, 43.083, 66.316
Unit cell angles	80.53, 74.52, 64.01

Refinement procedure

Resolution	19.330 - 2.000
R-factor	0.191
Rwork	0.189
R-free	0.23460
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4mur
RMSD bond length	0.018
RMSD bond angle	0.810
Data reduction software	XDS
Data scaling software	SCALA
Phasing software	PHENIX
Refinement software	PHENIX ((phenix.refine: dev_1538))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	19.330	2.110
High resolution limit [Å]	2.000	2.000
Rmerge	0.079	0.518
Number of reflections	25760
<I/σ(I)>	11	2.3
Completeness [%]	94.9	92.3
Redundancy	3.3	3.3

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	5.6		0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K, 1 mM CuCl2 and 20 mM D-Ala-D-Ala. Cryoprotectant: paratone, pH 5.6, VAPOR DIFFUSION, HANGING DROP