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Sequence specific (AATT) orientation of DAPI molecules at a unique minor groove binding site (position2) within a self-assembled 3D DNA lattice (4x5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.5 mL of 0.05 M HEPES pH 7.5 with 15 mM MgCl2, 1.0 mM spermidine, and 10% dioxan was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Crystal Properties Matthews coefficient Solvent content 6.49 81.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.507 α = 90 b = 69.507 β = 90 c = 59.552 γ = 120
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 PILATUS3 6M 2022-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.92 APS 19-ID
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 3.1 50 99.7 0.129 0.136 0.042 1 6.1 9.7 5774
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 3.1 3.15 97.3 1.629 1.755 0.627 0.644 6.7
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.11 42.37 5335 304 97.12 0.19728 0.19501 0.1982 0.23789 0.2365 RANDOM 138.397
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] 0.02 0.01 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.044 r_long_range_B_other 24.037 r_scangle_other 19.044 r_scbond_it 14.663 r_scbond_other 14.656 r_angle_refined_deg 2.066 r_angle_other_deg 1.647 r_chiral_restr 0.146 r_bond_other_d 0.068 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.044 r_long_range_B_other 24.037 r_scangle_other 19.044 r_scbond_it 14.663 r_scbond_other 14.656 r_angle_refined_deg 2.066 r_angle_other_deg 1.647 r_chiral_restr 0.146 r_bond_other_d 0.068 r_gen_planes_refined 0.011 r_bond_refined_d 0.006 r_gen_planes_other 0.001 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 855 Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing