9O8N

Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-03-15
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 63
Unit cell lengths	97.696, 97.696, 78.288
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	48.850 - 1.590
R-factor	0.1587
Rwork	0.158
R-free	0.17950
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.917
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (dev_5660)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.850	1.620
High resolution limit [Å]	1.590	1.590
Rmerge	0.196	2.870
Rmeas	0.201	2.939
Rpim	0.044	0.630
Total number of observations	1173267	60173
Number of reflections	57075	2815
<I/σ(I)>	13.3	1.6
Completeness [%]	100.0
Redundancy	20.6	21.4
CC(1/2)	0.999	0.308

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	4	291	Berkeley A1: 2200 mM Sodium chloride, 100 mM Tris HCl/ Sodium hydroxide pH 8.0, 50 mM Calcium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. plate 19707 A1 drop 1, Puck: PSL1213, Cryo: 80% crystallant + 20% glycerol.