9YL5

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil

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	2025-06-30
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	I 1 2 1
Unit cell lengths	97.126, 75.061, 180.117
Unit cell angles	90.00, 105.57, 90.00

Refinement procedure

Resolution	74.430 - 2.560
R-factor	0.2033
Rwork	0.201
R-free	0.24850
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	0.837
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5833: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	93.500	2.630
High resolution limit [Å]	2.560	2.560
Rmerge	0.115	0.948
Rmeas	0.131	1.085
Rpim	0.062	0.517
Total number of observations	165663	11914
Number of reflections	40030	2933
<I/σ(I)>	9.4	1.6
Completeness [%]	98.9
Redundancy	4.1	4.1
CC(1/2)	0.997	0.657

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	Morpheus B9: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 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. 2mM ligand added to protein prior to crystallization. plate 19802 B9 drop 1, Puck: PSL-2810, Cryo: direct