8DL3

Crystal structure of the human queuine salvage enzyme DUF2419, complexed with queuine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL12-2
Synchrotron site	SSRL
Beamline	BL12-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-06-25
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97946
Spacegroup name	P 1 21 1
Unit cell lengths	42.726, 136.759, 52.606
Unit cell angles	90.00, 90.33, 90.00

Refinement procedure

Resolution	42.760 - 2.260
R-factor	0.1587
Rwork	0.156
R-free	0.22210
Structure solution method	FOURIER SYNTHESIS
Starting model (for MR)	7ugk
RMSD bond length	0.007
RMSD bond angle	1.205
Data reduction software	HKL-3000 (v721.3)
Data scaling software	HKL-3000 (v721.3)
Refinement software	REFMAC (5.8.0222)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	45.000	45.000	2.290
High resolution limit [Å]	2.250	6.100	2.250
Rmerge	0.226	0.077	1.516
Rmeas	0.245	0.084	1.678
Rpim	0.095	0.032	0.705
Total number of observations	180879
Number of reflections	27661	1419	1304
<I/σ(I)>	4.1
Completeness [%]	97.9	98.3	94.5
Redundancy	6.5	6.9	5.2
CC(1/2)		0.996	0.478

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2M NaCl, 25% PEG3350, 0.1M Bis-Tris, pH 5.5