Experiment: 4Y1M

An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	0.2 mM RNA in 10 mm NaCacodylate, 50 mM NaCl, 10 mM MgCl2 with a mother liquor of 10% MPD, 40 mM Na cacodylate pH 7, 80 mM SrCl2, 20 mM MgCl2, 12 mM spermine tetra-HCl at 21 C. Native crystals were quickly cryo-protected in mother liquor plus 20% ethylene glycol prior to flash freezing in liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
4.83	74.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.384	α = 90
b = 159.384	β = 90
c = 277.108	γ = 120

Symmetry
Space Group	H 3 2

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		2014-06-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.769, 0.7692, 0.9999	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	3	123.6	100	0.116	20.2	11.3		27410

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	3	3.11	100		1.01	2.41	11.6

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	MAD	FREE R-VALUE	3	123.6	1.34	26818	1623	99.65	0.2186	0.2166	0.2349	0.2521	0.2692

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	17.05
f_angle_d	0.614
f_chiral_restr	0.067
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	3916
Solvent Atoms	72
Heterogen Atoms	138

Software

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