9TCA

Crystal Structure of a tRNA acceptor stem mimic at 1.94 A resolution

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I23
Synchrotron site	Diamond
Beamline	I23
Temperature [K]	80
Detector technology	PIXEL
Collection date	2023-12-15
Detector	DECTRIS PILATUS 12M
Wavelength(s)	3.024
Spacegroup name	P 21 21 21
Unit cell lengths	28.820, 32.380, 78.450
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	27.050 - 1.944
Rwork	0.247
R-free	0.27700
Structure solution method	SAD
RMSD bond length	0.008
RMSD bond angle	2.003
Data scaling software	XDS (0.7.9)
Phasing software	AutoSol
Refinement software	REFMAC (5.8.0430 (refmacat 0.4.105))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	27.050	27.050	1.990
High resolution limit [Å]	1.940	8.910	1.940
Rmerge	0.058	0.061	1.823
Rmeas	0.060	0.063	2.039
Rpim	0.014	0.013	0.872
Number of reflections	5588	76	346
<I/σ(I)>	25.8	76.8	1.2
Completeness [%]	97.2	98.1	88.5
Redundancy	23.3	35.3	8.9
CC(1/2)	0.972	0.999	0.440

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		292	FUSION (Molecular Dimensions Ltd) was used for screening crystallization conditions by the sitting drop vapor diffusion method (Gorrec & Bellini, 2022). Solutions containing the RNA samples (1 mM) in 100 mM HEPES buffer pH 8 and 10 mM MgCl2 were heated at 65 degrees C for 2 minutes, then cooled slowly to room temperature. The RNA solutions were mixed with FUSION solution in a 1:1 ratio for crystallization. The optimized crystallization conditions for the RNAs are listed in Table 1. All crystals grew at 19 degrees C and were cryoprotected in 20% glycerol before flash-cooling in liquid nitrogen.