9ZNH

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase 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	2025-06-07
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	C 1 2 1
Unit cell lengths	133.820, 75.050, 92.460
Unit cell angles	90.00, 113.27, 90.00

Refinement procedure

Resolution	46.730 - 2.340
R-factor	0.2166
Rwork	0.214
R-free	0.25940
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.773
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX ((2.0_5904: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.730	2.446
High resolution limit [Å]	2.340	2.340
Rmerge	0.061	0.450
Rmeas	0.066	0.485
Rpim	0.025	0.179
Number of reflections	26752	1338
<I/σ(I)>	15.24	4.799
Completeness [%]	75.0	30.34
Redundancy	6.95	7.14
CC(1/2)	0.998	0.960

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	Morpheus E12: 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 Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. BopeA.00730.a.B2.PW39381 at 13.8 mg/mL. The diffraction data where highly ansiotropic resulting in high B-factors. Therefore the anisotropically truncated data (staraniso) were used for refinement and both data sets were deposited. plate 19802 E12 drop 1, Puck: PSL-1009, Cryo: direct