☰ Navigation Tabs
Crystal structure of xanthine/guanine RNA aptamer (P1-12bp) with 3-methylxanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9M69 XBA12-XAN structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.08 M Potassium chloride
0.02 M Magnesium chloride hexahydrate
50% v/v (+/-)-2-Methyl-2,4-pentanediol
0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 1.96 37.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.37 α = 90 b = 22.6 β = 90 c = 44.96 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 EIGER2 S 9M 2023-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97895 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 2.18 34.73 99.9 0.154 0.065 0.993 8.5 11.9 11974 47.71
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 2.18 2.24 100 1.251 0.561 0.68
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 2.18 30.56 1.34 11873 599 99.56 0.2468 0.2451 0.2459 0.2788 0.2846 58.64
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 26.1011 f_angle_d 1.0967 f_chiral_restr 0.0433 f_plane_restr 0.0054 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1740 Solvent Atoms 52 Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing