8AY0

Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in complex with murein tripeptide

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04
Synchrotron site	Diamond
Beamline	I04
Temperature [K]	100
Detector technology	PIXEL
Collection date	2015-02-14
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.9795
Spacegroup name	P 1
Unit cell lengths	60.855, 61.310, 124.073
Unit cell angles	78.09, 82.67, 61.60

Refinement procedure

Resolution	60.739 - 1.510
Rwork	0.184
R-free	0.22130
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4faj
RMSD bond length	0.008
RMSD bond angle	1.502
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0352)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	60.740	60.670	1.540
High resolution limit [Å]	1.510	8.270	1.510
Rmerge	0.053	0.021	0.759
Rmeas	0.075	0.030	1.073
Rpim	0.053	0.021	0.759
Number of reflections	233391	1437	11306
<I/σ(I)>	8.4
Completeness [%]	96.3
Redundancy	2.2	2.2	2.2
CC(1/2)	0.998	0.998	0.572

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % PEG 3350 and 2.5 % DMSO with 1 microl of protein at 13 mg.ml-1 .