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Crystal Structure of inosine-substituted duplex DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 Droplets (2 uL) containing oligonucleotide (0.23 mM), sodium cacodylate (25 mM, pH 6.5), magnesium acetate (12.5 mM), and 2-methyl-2,4-pentanediol (MPD, 20% v/v) that were equilibrated against a 1 mL
reservoir of sodium cacodylate (50 mM, pH 6.5), magnesium acetate (25 mM), and MPD (40%)
v/v)
Crystal Properties Matthews coefficient Solvent content 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.19 α = 90 b = 35.043 β = 90 c = 41.336 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 MARMOSAIC 225 mm CCD 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97625 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.36 50 99.1 0.073 0.035 30.57 7.7 11019 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.41 95 0.343 0.133 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.36 26.73 10415 569 99.47 0.14922 0.1475 0.1543 0.1809 0.1928 RANDOM 11.216
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] 0.33 -0.59 0.26
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.107 r_long_range_B_other 3.628 r_angle_other_deg 1.626 r_angle_refined_deg 1.607 r_scangle_other 1.436 r_scbond_it 1.008 r_scbond_other 1.005 r_chiral_restr 0.09 r_gen_planes_refined 0.036 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.107 r_long_range_B_other 3.628 r_angle_other_deg 1.626 r_angle_refined_deg 1.607 r_scangle_other 1.436 r_scbond_it 1.008 r_scbond_other 1.005 r_chiral_restr 0.09 r_gen_planes_refined 0.036 r_bond_refined_d 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.002 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 400 Solvent Atoms 179 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing