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Crystal Structure of inosine-substituted decamer duplex DNA (I4)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 279 Droplets (2 uL) containing
oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), magnesium acetate (12.5 mM), and 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 2.01 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.884 α = 90.25 b = 32.798 β = 107.32 c = 34.034 γ = 111.04
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 9M 2016-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9184 APS 21-ID-D
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 1.55 32.24 97.1 0.073 0.053 28.7 5.9 13618 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 1.55 1.58 90 1 0.434 4.5
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 SAD THROUGHOUT 1.55 32.24 12813 801 94.82 0.20857 0.20696 0.2082 0.23358 0.2344 RANDOM 22.471
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] 1.7 0.37 0.73 -0.8 -0.14 -1.11
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.919 r_long_range_B_other 5.825 r_scangle_other 3.667 r_scbond_other 2.726 r_scbond_it 2.725 r_angle_refined_deg 2.085 r_angle_other_deg 1.68 r_chiral_restr 0.11 r_gen_planes_refined 0.037 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.919 r_long_range_B_other 5.825 r_scangle_other 3.667 r_scbond_other 2.726 r_scbond_it 2.725 r_angle_refined_deg 2.085 r_angle_other_deg 1.68 r_chiral_restr 0.11 r_gen_planes_refined 0.037 r_bond_refined_d 0.012 r_gen_planes_other 0.007 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 792 Solvent Atoms 156 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing