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Crystal structure of Ade1301 DNA aptamer (one strand) bound to adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other I-SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.05 M Calcium Chloride dihydrate
0.1 M Bis-Tris pH 6.5
30% w/v Polyethylene Glycol Monomethyl ether 550
20% w/v Benzamidine HCl
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.31 α = 90 b = 63.05 β = 90 c = 76.25 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 PIXEL DECTRIS EIGER X 16M 2024-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979183 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 2.93 50.31 98 0.127 0.04 0.997 12 11.2 5480 93.1
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 2.93 3.01 1.583 0.552 0.69
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 2.93 26.71 1.35 5424 279 97.84 0.2379 0.2368 0.2378 0.255 0.2547 90.77
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 35.3786 f_angle_d 0.8437 f_chiral_restr 0.0461 f_bond_d 0.006 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1606 Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing