9ZNJ

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 6,7-dimethyl-8-(1'-D-ribityl) lumazine

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	2025-11-01
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	C 1 2 1
Unit cell lengths	135.448, 75.416, 94.461
Unit cell angles	90.00, 114.38, 90.00

Refinement procedure

Resolution	46.910 - 2.150
R-factor	0.2262
Rwork	0.224
R-free	0.26060
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.623
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5904: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.910	2.220
High resolution limit [Å]	2.150	2.150
Rmerge	0.097	1.511
Rmeas	0.106	1.646
Rpim	0.041	0.646
Total number of observations	318307	26045
Number of reflections	47090	4048
<I/σ(I)>	10.7	1.6
Completeness [%]	99.6
Redundancy	6.8	6.4
CC(1/2)	0.999	0.824

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. 24 hour soak with 2 mM 6,7-dimethyl-8-(1'-D-ribityl) lumazine. plate 19802 B12, Puck: PSL-0104, Cryo: direct