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Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QS6 helical parameters taken from 2qs6, 1rsb experimental model PDB 1RSB helical parameters taken from 2qs6, 1rsb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 286 0.8mM of the oligonucleotide, 20mM sodium cacodylate buffer (pH = 6.5), 3mM spermine, 100mM N-ethylaniline hydrochloride and 5% MPD, equilibrated against a reservoir with 30% MPD.
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.756 α = 90 b = 42.898 β = 90.04 c = 99.422 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2005-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.9762 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.13 33.14 99.6 0.107 7.48 3.7 1888 144
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.13 3.241 99.35 0.585 1.88 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 helical parameters taken from 2qs6, 1rsb 3.13 33.14 1773 107 99.26 0.1481 0.14582 0.1449 0.19979 0.2038 RANDOM 138.561
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] -9.92 93.61 41.24 -31.32
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 26.717 r_long_range_B_refined 26.712 r_scangle_other 24.345 r_scbond_it 16.55 r_scbond_other 16.542 r_angle_other_deg 6.678 r_angle_refined_deg 0.939 r_chiral_restr 0.068 r_bond_other_d 0.023 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 26.717 r_long_range_B_refined 26.712 r_scangle_other 24.345 r_scbond_it 16.55 r_scbond_other 16.542 r_angle_other_deg 6.678 r_angle_refined_deg 0.939 r_chiral_restr 0.068 r_bond_other_d 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 600 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling