Experiment: 4Y1I

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION		FREE R-VALUE	2.85	55.9	1.35	19804	2125	89.62	0.1957	0.1928	0.2235

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.