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Structure of an alternating AT 16-mer: 5'-GCTGGATATATCCAGC-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 288 1 mM DNA duplex annealed in 7.5 mM HEPES, pH=6.6 mixed at a 1:1 ratio with well solution containing 10 mM HEPES, pH=8.6, 600 mM CaCl2, 38% PEG200
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.769 α = 90 b = 38.769 β = 90 c = 159.771 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 2022-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.92010 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 1.08 26.63 98.5 0.01722 0.02436 0.01722 0.999 22.55 2 20060 15.5
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 1.08 1.119 92.88 0.1479 0.2092 0.1479 0.939 6.48 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 1.08 26.63 1.33 20000 1996 97.87 0.2035 0.2012 0.2032 0.2247 0.2241 21.64
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 33.2802 f_angle_d 2.0651 f_chiral_restr 0.1188 f_plane_restr 0.0342 f_bond_d 0.0204
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 325 Solvent Atoms 94 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing