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Sequence specific (AATT) orientation of DAPI molecules at a unique minor groove binding site (position1) within a self-assembled 3D DNA lattice (4x6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.5 mL of 0.05 M Na cacodylate pH 6.5 with 1.0 mM spermine, 2.0 mM CoH18N6, 30 mM CaCl2, and 2.0 M LiCl was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Crystal Properties Matthews coefficient Solvent content 6.14 79.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.395 α = 90 b = 68.395 β = 90 c = 58.132 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 2.8 50 97.2 0.118 0.124 0.038 1 6.9 9.7 7272
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 2.8 2.85 76.9 1.088 1.156 0.382 0.73 7.8
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 2.8 41.52 6763 364 95.42 0.19491 0.19245 0.1956 0.24397 0.2501 RANDOM 83.909
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] -0.03 -0.01 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.889 r_long_range_B_other 14.884 r_scangle_other 12.514 r_scbond_it 9.089 r_scbond_other 9.085 r_angle_refined_deg 2.329 r_angle_other_deg 0.492 r_chiral_restr 0.155 r_gen_planes_refined 0.013 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.889 r_long_range_B_other 14.884 r_scangle_other 12.514 r_scbond_it 9.089 r_scbond_other 9.085 r_angle_refined_deg 2.329 r_angle_other_deg 0.492 r_chiral_restr 0.155 r_gen_planes_refined 0.013 r_bond_refined_d 0.007 r_bond_other_d 0.007 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 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing