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Crystal structure of Ade1304 DNA aptamer (1304b9) bound to adenosine with barium ions
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.2 M Calcium chloride dihydrate,
0.05 M HEPES sodium pH 7.5,
30% v/v Polyethylene glycol 400,
0.002 M Spermine,
0.01 M barium chloride
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.795 α = 90 b = 58.795 β = 90 c = 122.411 γ = 120
Symmetry Space Group P 62 2 2
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 2023-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 1.541900 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 50.92 89.5 0.06 0.01 0.999 27.6 31.7 27593
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 1.845 0.552 0.469
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 SAD FREE R-VALUE 1.6 40.8 1.34 15169 766 88.56 0.2342 0.232 0.2328 0.2891 0.2829 35.14
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 34.0554 f_angle_d 1.2464 f_chiral_restr 0.0607 f_plane_restr 0.0099 f_bond_d 0.0098
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 906 Solvent Atoms 124 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement PHENIX refinement PDB_EXTRACT data extraction autoPX data reduction autoPROC data scaling AutoSol phasing