Experiment: 4Y1I

Lactococcus lactis yybP-ykoY Mn riboswitch bound to Mn2+

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	RNA solution: 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, 2.5 mM MnCl2, Mother liquor: 14% (+/-)-2-methyl-2,4-pentanediol (MPD) , 40 mM Na cacodylate pH 7.0, 80 mM NaCl, 20 mM BaCl2, 12 mM spermine tetra-HCl, at 21 C, with 1:2 RNA: mother liquor drop ratio. Cryoprotection: 20% PEG-400 and 0.1 mM MnCl2 overnight soak.

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.285	α = 90
b = 127.881	β = 93.37
c = 115.324	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	294	PIXEL	PSI PILATUS 6M		2014-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.892	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.85	55.9	92	0.136	20.5	4.1		20952

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.95	92		0.47	2.87	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION		FREE R-VALUE	2.85	55.9	1.35	19804	2125	89.62	0.1957	0.1928	0.1992	0.2235	0.2273

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.844
f_angle_d	0.425
f_chiral_restr	0.018
f_bond_d	0.013
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	4284
Solvent Atoms	56
Heterogen Atoms	111

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing