5XWG

Crystal structure of a novel RNA motif that allows for precise positioning of a metal ion

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	sodium cacodylate, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, strontium chloride

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.544	α = 90
b = 80.544	β = 90
c = 80.544	γ = 90

Symmetry
Space Group	I 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2013-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.91972	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.002	56.953	99.6	19.3	11.1		3373			101.31

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	3.1	100		0.337		11.4

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	3.002	21.526	1.99	3364	305	99.53	0.2177	0.217	0.2255	90.52

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	9.368
f_angle_d	1.439
f_chiral_restr	0.163
f_plane_restr	0.025
f_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	320
Solvent Atoms
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
AutoSol	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.