9TCG

Crystal Structure of a prebiotic tRNA acceptor stem mimic

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04
Synchrotron site	Diamond
Beamline	I04
Temperature [K]	80
Detector technology	PIXEL
Collection date	2023-12-15
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.916
Spacegroup name	P 65 2 2
Unit cell lengths	32.007, 32.007, 281.333
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	46.889 - 2.520
Rwork	0.258
R-free	0.29550
Structure solution method	SAD
RMSD bond length	0.005
RMSD bond angle	1.265
Data scaling software	XDS (0.8.2)
Phasing software	PHENIX (0.7.1)
Refinement software	REFMAC (5.8.0431 (refmacat 0.4.105))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	46.890	46.890	2.600
High resolution limit [Å]	2.500	9.020	2.500
Rmerge	0.088	0.035	6.622
Rmeas	0.090	0.036	6.783
Rpim	0.020	0.009	1.462
Number of reflections	3624	129	366
<I/σ(I)>	24.8	70.3	0.6
Completeness [%]	100.0	99.9	100
Redundancy	33.2	19.5	35.8
CC(1/2)	1.000	1.000	0.388

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.