8B02

Crystal structure of the dsRBD domain of tRNA-dihydrouridine(20) synthase from Amphimedon queenslandica

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 2
Synchrotron site	SOLEIL
Beamline	PROXIMA 2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-11-16
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.98011
Spacegroup name	P 1 21 1
Unit cell lengths	29.077, 56.895, 63.587
Unit cell angles	90.00, 93.05, 90.00

Refinement procedure

Resolution	29.040 - 1.676
R-factor	0.2047
Rwork	0.203
R-free	0.22780
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4wft
RMSD bond length	0.009
RMSD bond angle	1.020
Data reduction software	autoPROC (1.0.5)
Data scaling software	XDS (Jan 10, 2022 (BUILT 20220220))
Phasing software	PHASER (2.8.2)
Refinement software	BUSTER (2.10.4 (8-JUN-2022))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	42.373	1.705
High resolution limit [Å]	1.676	1.676
Rmerge	0.074	0.975
Rmeas	0.090	1.245
Rpim	0.051	0.762
Number of reflections	23361	963
<I/σ(I)>	7.8	0.8
Completeness [%]	97.9	79.7
Redundancy	2.9	2
CC(1/2)	0.997	0.351

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	0.1 M Hepes pH 7.5, 1.4 M tri-sodium citrate, 15 mg/ml protein in 50 mM Tris, pH 8 300 mM NaCl 5mM mercaptoethanol