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The DNA 16-mer sequence 5'-GCTGCGTTAACGCAGC-3' bound by a DB1992 stacked dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8V4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 295 10mM HEPES, pH=8.6, 600mM CaCl2, 41% PEG200 mixed 1:1 with 1mM DNA duplex
Crystal Properties Matthews coefficient Solvent content 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.345 α = 90 b = 38.345 β = 90 c = 162.141 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 EIGER X 16M 2023-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979340 NSLS-II 17-ID-2
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 1.49 32.53 99.28 0.05583 0.05887 0.01832 0.999 22.13 10.8 7906 16.94
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 1.49 1.543 99.87 0.5523 0.5799 0.1751 0.947 4.18 10.9
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 1.49 32.53 1.34 7864 784 99.32 0.2273 0.2245 0.2249 0.2492 0.2483 25.04
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 32.2557 f_angle_d 1.7471 f_chiral_restr 0.0852 f_bond_d 0.0199 f_plane_restr 0.019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 325 Solvent Atoms 69 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing