4R8I

High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	After thorough optimization of crystallization conditions needle shaped crystals (approx. 300x50x50um) could be obtained by mixing 1uL of the NOX-E36-CCL2 complex (in 20 mM HEPES pH 7.4, 100 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2) with 1uL of a solution containing 40 mM Na cacodylate pH 5.5, 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2 and subsequent vapor-diffusion equilibration against 1 mL of reservoir (35% (v/v) MPD, 5 mM KCl, 1 mM MgCl2 and 1 mM CaCl2). Crystals used for data collection grew within three weeks at 277K. VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.912	α = 90
b = 108.912	β = 90
c = 34.812	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS PILATUS 6M		2013-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.978	EMBL/DESY, HAMBURG	X13

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	2.05	100	99.2				24915	-3		36.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	77.01	12058	1348	97.9	0.20504	0.20003	0.201	0.24971	0.2498	RANDOM	32.728

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]
0.21			0.21		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.662
r_dihedral_angle_4_deg	25.514
r_dihedral_angle_3_deg	14.378
r_dihedral_angle_1_deg	5.36
r_long_range_B_refined	5.024
r_mcangle_it	3.633
r_mcbond_it	2.098
r_angle_refined_deg	1.609
r_scbond_it	1.536
r_chiral_restr	0.074

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	544
Nucleic Acid Atoms	853
Solvent Atoms	111
Heterogen Atoms	7

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	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 R01GM157729.