6TIX

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID23-2
Synchrotron site	ESRF
Beamline	ID23-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-04-13
Detector	DECTRIS PILATUS3 X 2M
Wavelength(s)	0.8731
Spacegroup name	P 1
Unit cell lengths	48.172, 84.035, 87.099
Unit cell angles	112.92, 95.31, 104.57

Refinement procedure

Resolution	45.693 - 2.800
Rwork	0.228
R-free	0.29020
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5lp4
RMSD bond length	0.004
RMSD bond angle	1.299
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	REFMAC (5.8.0258)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	45.693	2.950
High resolution limit [Å]	2.800	2.800
Rmerge	0.108	0.452
Rmeas		0.640
Rpim	0.097	0.452
Number of reflections	27215	4118
<I/σ(I)>	4.1	1.2
Completeness [%]	92.9	96.7
Redundancy	2.1	2.1
CC(1/2)	0.991	0.677

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		296	Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000). The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam)