6S7D

Self-complementary duplex DNA containing an internucleoside phosphoroselenolate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	The crystallization solution contained 1 uL of 2 mM oligonucleotide and 6 uL of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 40 mM Na-cacodylate pH 6, 12 mM Spermine tetra-HCl, 80 mM NaCl and 20 mM BaCl2. This was equilibrated against 100 uL of 35% (v/v) 2-methyl-2,4-pentanediol. Crystals grew in approximately 1-2 weeks and were grown using the sitting-drop method at 291 K.

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.642	α = 90
b = 38.642	β = 90
c = 79.307	γ = 120

Symmetry
Space Group	P 31 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	100	PIXEL	DECTRIS PILATUS3 6M		2019-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9596	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.45	25.57	98.4	0.05	0.06	0.032	0.998	12.5	3		12548	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47	98.7		0.556	0.674	0.375	0.741		2.9

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	SAD	FREE R-VALUE	1.45	25.57	3.79	12530	579	98.31	0.1919	0.1849	0.2366	25.54

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	20.1052
f_angle_d	0.9357
f_chiral_restr	0.0785
f_plane_restr	0.0092
f_bond_d	0.0089

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	60
Heterogen Atoms	19

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
xia2	data scaling
DIALS	data reduction
SHELXCD	phasing

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.