7TDC

Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, calcium ions

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-03-21
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.9791
Spacegroup name	P 32 1 2
Unit cell lengths	65.006, 65.006, 101.274
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	56.300 - 2.460
R-factor	0.215
Rwork	0.211
R-free	0.24700
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2hoj
RMSD bond length	0.005
RMSD bond angle	1.116
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	56.300	2.560
High resolution limit [Å]	2.460	2.460
Rmerge	0.098	3.730
Number of reflections	9133	1026
<I/σ(I)>	13.9	0.7
Completeness [%]	99.9	99.9
Redundancy	13.8	12.9

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6	291	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 0.75 mM TPPc. Reservoir solution was 50 mM sodium cacodylate, pH 6.0, 0.3 M NH4Cl, 10 mm CaCl2, and 30% (v/v) PEG2000