4P5J

Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ALS BEAMLINE 4.2.2
Synchrotron site	ALS
Beamline	4.2.2
Temperature [K]	100
Detector technology	CMOS
Collection date	2013-10-21
Detector	RDI CMOS_8M
Wavelength(s)	1.0972
Spacegroup name	I 2 2 2
Unit cell lengths	55.270, 101.570, 111.610
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	28.871 - 1.991
R-factor	0.2088
Rwork	0.206
R-free	0.23960
Structure solution method	SAD
RMSD bond length	0.011
RMSD bond angle	1.791
Refinement software	PHENIX ((phenix.refine: 1.8.4_1496))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	66.000	2.030
High resolution limit [Å]	1.990	1.990
Rmerge	0.054	0.820
Number of reflections	41343
<I/σ(I)>	21.71	2.19
Completeness [%]	99.4	94.7
Redundancy	7.45

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room temperature. After cooling, Spermidine was added to 0.5 mM. The reaction was centrifuged for 10 minutes at 13000 x g and then used in sitting-drop vapor diffusion crystallization at 4?C. 1 ?L of RNA solution was combined with 2 ?L of 10% MPD, 40 mM Na-Cacodylate pH 6.0, 12 mM Spermine, 80 mM NaCl, and 20 mM MgCl2. The well solution was 20-35% MPD. Crystals appeared and grew to full size over the course of 1-2 days.