5W1Z

Crystal Structure of inosine-substituted decamer duplex DNA (I4)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	279	Droplets (2 uL) containing oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), magnesium acetate (12.5 mM), and MPD (20% v/v) that were equilibrated against a 1 mL reservoir of sodium cacodylate (50 mM, pH 6.5), magnesium acetate (25 mM), and MPD (40% v/v)

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.884	α = 90.25
b = 32.798	β = 107.32
c = 34.034	γ = 111.04

Symmetry
Space Group	P 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 EIGER X 9M		2016-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9184	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.55	32.24	97.1	0.073	0.053	28.7	5.9		13618		5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	90		1	0.434		4.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.55	32.24	12813	801	94.82	0.20857	0.20696	0.23358	RANDOM	22.471

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]
1.7	0.37	0.73	-0.8	-0.14	-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	5.919
r_long_range_B_other	5.825
r_scangle_other	3.667
r_scbond_other	2.726
r_scbond_it	2.725
r_angle_refined_deg	2.085
r_angle_other_deg	1.68
r_chiral_restr	0.11
r_gen_planes_refined	0.037
r_bond_refined_d	0.012
r_gen_planes_other	0.007
r_bond_other_d	0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	792
Solvent Atoms	156
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing