4P5J

Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room temperature. After cooling, Spermidine was added to 0.5 mM. The reaction was centrifuged for 10 minutes at 13000 x g and then used in sitting-drop vapor diffusion crystallization at 4?C. 1 ?L of RNA solution was combined with 2 ?L of 10% MPD, 40 mM Na-Cacodylate pH 6.0, 12 mM Spermine, 80 mM NaCl, and 20 mM MgCl2. The well solution was 20-35% MPD. Crystals appeared and grew to full size over the course of 1-2 days.

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.27	α = 90
b = 101.57	β = 90
c = 111.61	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CMOS	RDI CMOS_8M		2013-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.0972	ALS	4.2.2

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	1.99	66	99.4	0.054	21.71	7.45		41343		2

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	1.99	2.03	94.7		0.82	2.19

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.9912	28.871	1.34	41334	3790	99.46	0.2088	0.2057	0.2396	Random

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	14.148
f_angle_d	1.791
f_chiral_restr	0.082
f_plane_restr	0.013
f_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1785
Solvent Atoms	126
Heterogen Atoms	100

Software

Software
Software Name	Purpose
PHENIX	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.