6XV5

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

This is a non-PDB format compatible entry.

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	2018-09-09
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.9795
Spacegroup name	P 21 21 21
Unit cell lengths	56.265, 147.772, 164.523
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	109.937 - 2.673
Rwork	0.213
R-free	0.28510
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6tii
RMSD bond length	0.003
RMSD bond angle	1.279
Data reduction software	XDS
Data scaling software	STARANISO
Phasing software	PHASES
Refinement software	REFMAC (5.8.0258)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	109.937	7.331
High resolution limit [Å]	2.670	2.701
Rmerge	0.133	0.040
Number of reflections	38541	2108
<I/σ(I)>	12.2
Completeness [%]	100.0
Redundancy	13.1
CC(1/2)	0.999	0.999

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION		296	Crystals were grown in a condition containing 1 uL of 1 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM ertapenem) and 2 uL of reservoir solution (0.5 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5).