5W20

Crystal Structure of inosine-substituted duplex DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	Droplets (2 uL) containing oligonucleotide (0.23 mM), sodium cacodylate (25 mM, pH 6.5), magnesium acetate (12.5 mM), and 2-methyl-2,4-pentanediol (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
2.05	40.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.19	α = 90
b = 35.043	β = 90
c = 41.336	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2015-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97625	APS	21-ID-F

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	1.36	50	99.1	0.073	0.035	30.57	7.7		11019		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	1.36	1.41	95		0.343	0.133		7.6

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		THROUGHOUT	1.36	26.73	10415	569	99.47	0.14922	0.1475	0.1809	RANDOM	11.216

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]
0.33			-0.59		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	4.107
r_long_range_B_other	3.628
r_angle_other_deg	1.626
r_angle_refined_deg	1.607
r_scangle_other	1.436
r_scbond_it	1.008
r_scbond_other	1.005
r_chiral_restr	0.09
r_gen_planes_refined	0.036
r_bond_refined_d	0.012
r_gen_planes_other	0.006
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	400
Solvent Atoms	179
Heterogen Atoms	6

Software

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