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Structure of the DNA duplex d(AAATTT)2 with the potential antiparasitic drug 6XV at 1.25 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other AAATTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277.1 10 mM Magnesium Acetate
Crystal Properties Matthews coefficient Solvent content 2.22 44.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.33 α = 90 b = 40.25 β = 93.67 c = 72.423 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 2016-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9787 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.247 36.14 92.9 0.069 0.991 14.1 6.1 16801 5.519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 89.8 0.227 0.965 5.5 5.5
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 AAATTT 1.25 36.14 15741 853 92.51 0.12284 0.12053 0.1302 0.16688 0.1726 RANDOM 11.883
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] 0.28 0.45 -0.04 -0.29
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 20.239 r_rigid_bond_restr 13.64 r_sphericity_bonded 6.768 r_angle_refined_deg 2.518 r_long_range_B_refined 2.382 r_angle_other_deg 1.894 r_long_range_B_other 1.824 r_scangle_other 1.704 r_scbond_it 1.457 r_scbond_other 1.456
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 20.239 r_rigid_bond_restr 13.64 r_sphericity_bonded 6.768 r_angle_refined_deg 2.518 r_long_range_B_refined 2.382 r_angle_other_deg 1.894 r_long_range_B_other 1.824 r_scangle_other 1.704 r_scbond_it 1.457 r_scbond_other 1.456 r_chiral_restr 0.122 r_gen_planes_refined 0.038 r_bond_refined_d 0.022 r_bond_other_d 0.006 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 480 Solvent Atoms 165 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling