Experiment: 4Y1J

Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	0.1-0.2 mM RNA in 10 mM Na Cacodylate pH 7, 50 mM NaCl, 10 mM MgCl2, 2.5 mM MnCl2. Crystallized in about 2 months with a mother liquor of 40 mM Na cacodylate pH 6, 15% MPD, 80 mM SrCl2, 12 mM spermine tetra-HCl at 21 C. Crystals were cryo-protected by addition of 20% PEG-400 directly before freezing.

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.419	α = 116.21
b = 62.51	β = 101.83
c = 69.969	γ = 98.83

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	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	0.769	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	2.24	47.4	90	0.053	17.6	3.2		32334

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	2.24	2.32	95		0.55	2.1	3.2

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	SAD	FREE R-VALUE	2.24	47.4	0.44	29646	1742	89.06	0.2017	0.1993	0.1998	0.2415	0.2411

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	15.759
f_angle_d	1.038
f_chiral_restr	0.044
f_plane_restr	0.007
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	4280
Solvent Atoms	209
Heterogen Atoms	140

Software

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