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Crystal structure of xanthine/guanine RNA aptamer (P1-12bp) with uric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other XBA12-XAN structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 0.08 M Potassium chloride
0.02 M Magnesium chloride hexahydrate
52% v/v (+/-)-2-Methyl-2,4-pentanediol
0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.657 α = 90 b = 44.909 β = 90 c = 207.198 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 2023-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 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 2.52 207.2 99.8 0.096 0.043 0.997 11.2 10.6 7805 47.05
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 2.52 2.59 100 0.623 0.32 0.864
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 2.52 51.8 1.34 7699 344 99.01 0.2494 0.247 0.2424 0.303 0.2989 52.88
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 25.7997 f_angle_d 0.7133 f_chiral_restr 0.0312 f_plane_restr 0.0037 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1740 Solvent Atoms 58 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing