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The 24mer DNA Duplex 5'-GCTGGAAAGTTTAAACTTTCCAGC-3' Bound by the Diamidine DB2457 at Single G Sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9CJW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.62 295 0.8mM stock DNA solution in 7.5 mM HEPES, pH=6.6 buffer mixed 1:1 with well solution containing 10 mM HEPES, pH=8.6, 600 mM CaCl2, 42% PEG200
Crystal Properties Matthews coefficient Solvent content 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.28 α = 90 b = 39.28 β = 90 c = 480.772 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 PILATUS 6M 2023-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977410 ALS 5.0.1
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 1.68 33.93 99.72 0.06656 0.06912 0.01839 1 24.52 14.1 17320 20.68
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 1.68 1.74 99.34 0.6849 0.7103 0.1864 0.972 3.63 14.2
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 1.68 33.93 1.35 17283 1726 99.75 0.217 0.2128 0.2169 0.2557 0.2593 33.46
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 31.9149 f_angle_d 2.0193 f_chiral_restr 0.09 f_plane_restr 0.0194 f_bond_d 0.0182
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 978 Solvent Atoms 166 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing