7TZU

Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-2
Synchrotron site	NSLS-II
Beamline	17-ID-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-02-01
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.9793
Spacegroup name	P 32 1 2
Unit cell lengths	61.702, 61.702, 102.789
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	29.550 - 2.870
R-factor	0.2336
Rwork	0.229
R-free	0.26960
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2hoj
RMSD bond length	0.004
RMSD bond angle	0.748
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER (1.14-3260)
Refinement software	PHENIX (1.14-3260)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	30.000	2.920
High resolution limit [Å]	2.870	2.870
Rmerge	0.136	1.774
Rpim	0.042	0.583
Number of reflections	5295	267
<I/σ(I)>	32	0.9
Completeness [%]	99.8	100
Redundancy	11.8	9.7
CC(1/2)	0.944	0.637

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		291	The RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.7 mM compound 39. Reservoir solution was 50 mM Bis-Tris, pH 6.5, 0.45 M ammonium chloride, 10 mm MnCl2, and 30% (w/v) PEG2000