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Crystal structure of Ade1304 DNA aptamer (Ade1304b) bound to AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Ba SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 291 0.2 M Calcium chloride dihydrate,
0.05 M HEPES sodium pH 7.8,
28% v/v Polyethylene glycol 400,
0.002 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.948 α = 90 b = 200.474 β = 98.087 c = 40.238 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 S 9M 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
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 2.39 100.24 99.1 0.133 0.055 0.987 8.1 6.7 15979 51.13
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 2.39 2.52 1.667 0.716 0.622 1.2
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 2.39 33.41 1.37 15719 823 97.69 0.2199 0.217 0.214 0.2739 0.2717 57.56
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 35.1354 f_angle_d 1.028 f_chiral_restr 0.0502 f_bond_d 0.0067 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3124 Solvent Atoms 143 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing