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DB1976 Bound to the DNA Sequence 5'-CGCGAATTCGCG-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 40 mM Sodium Cacodylate pH=6.0, 12 mM Spermine tetrahydrochloride, 12 mM NaCl, 80 mM KCl, 10% MPD mixed in a 1:1 ratio with 1 mM DNA duplex annealed in the presence of ligand. Well solution for vapor diffusion was 40% MPD
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.442 α = 90 b = 41.286 β = 90 c = 65.719 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2022-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000030 ALS 8.2.1
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 1.79 34.96 98.52 0.03026 0.03272 0.01215 0.999 31.49 7.6 6849 38.62
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 1.79 1.854 99.56 0.5558 0.5952 0.2102 0.963 4.31 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.79 34.96 1.35 6843 684 98.52 0.2203 0.2171 0.2173 0.2471 0.2482 45.34
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 29.1857 f_angle_d 1.6535 f_chiral_restr 0.0766 f_plane_restr 0.0161 f_bond_d 0.0134
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 486 Solvent Atoms 32 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing