9CFN

Crystal structure of an exoribonuclease-resistant RNA from a Tombusvirus-like associated RNA

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-07-14
Detector	DECTRIS EIGER2 X 9M
Wavelength(s)	0.979
Spacegroup name	C 1 2 1
Unit cell lengths	107.637, 42.392, 84.491
Unit cell angles	90.00, 103.62, 90.00

Refinement procedure

Resolution	41.060 - 2.900
R-factor	0.2214
Rwork	0.217
R-free	0.25810
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.503
Data reduction software	XDS
Data scaling software	STARANISO (v3.352 5-Apr-2024)
Phasing software	PHENIX (1.20.1_4487)
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	41.060	3.004
High resolution limit [Å]	2.900	2.900
Rmerge	0.101	0.837
Rmeas	0.118	0.974
Rpim	0.060	0.491
Number of reflections	8421	494
<I/σ(I)>	10.53	1.71
Completeness [%]	87.3	58.81
Redundancy	3.7	6.5
CC(1/2)	0.981	0.817

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	well solution: 0.02 M Magnesium chloride hexahydrate 0.05 M Sodium cacodylate trihydrate pH 7.0 15% v/v 2-Propanol 0.001 M Hexammine cobalt(III) chloride 0.001 M Spermine 5 mg/mL RNA was dissolved in: 2.5 mM MgCl2 10 mM HEPES-KOH pH 7.5 0.5 mM spermidine 300 nL sitting drops were set up using the mosquito with a 1:1 well:RNA ratio