6GIM

Structure of the DNA duplex d(AAATTT)2 with [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)-4-((4,5-dihydro-1H-imidazol-2- yl)amino)benzamide] - (drug JNI18)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Idealised DNA model from TURBO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	10 mM magnesium acetate, 0.1 mM spermine, 5% 2-methyl-2,4-pentanediol (MPD); equilibrated against 20% MPD reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.304846	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.63	α = 90
b = 40.47	β = 93.91
c = 72.255	γ = 90

Symmetry
Space Group	I 1 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 PILATUS 6M		2017-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9791	ALBA	XALOC

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	1.43	36.04	99.5	0.073	0.081	0.033	0.995	2.79	4		12256			12.7

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	1.43	7.81	99.7		0.581	0.642	0.376	0.858	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	Idealised DNA model from TURBO	1.43	36.04	11306	557	96.79	0.14585	0.14342	0.19286	RANDOM	16.164

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]
0.42		0.71	-0.63		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	15.162
r_sphericity_bonded	8.746
r_dihedral_angle_2_deg	8.68
r_rigid_bond_restr	3.497
r_long_range_B_refined	3.07
r_long_range_B_other	2.91
r_scangle_other	2.751
r_scbond_it	2.228
r_scbond_other	2.227
r_angle_refined_deg	1.937
r_angle_other_deg	1.682
r_chiral_restr	0.088
r_gen_planes_refined	0.023
r_bond_refined_d	0.012
r_bond_other_d	0.006
r_gen_planes_other	0.003
r_dihedral_angle_1_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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	480
Solvent Atoms	96
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing