6TUD

Crystal structure of Y. pestis penicillin-binding protein 3

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04-1
Synchrotron site	Diamond
Beamline	I04-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-01-17
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.9196
Spacegroup name	P 41 21 2
Unit cell lengths	100.800, 100.800, 314.409
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	29.640 - 3.000
Rwork	0.244
R-free	0.27640
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6syn
RMSD bond length	0.002
RMSD bond angle	1.197
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]	29.640	3.150
High resolution limit [Å]	3.000	3.000
Rmerge	0.200	1.099
Rpim	0.071	0.518
Number of reflections	33546	4365
<I/σ(I)>	9.1	1.4
Completeness [%]	99.9	100
Redundancy	10
CC(1/2)	0.997	0.941

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		296	1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) Crystals were then dehydrated by replacing 50% of the reservoir solution with 50% PEG10000