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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)
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1488 0.19286 0.2012 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
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