☰ Navigation Tabs
Crystal structure of Adenine DNA aptamer bound with adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8K0W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.08 M Sodium chloride,
0.02 M Magnesium chloride hexahydrate
0.04 M Sodium cacodylate trihydrate pH 6.0
35% v/v (+/-)-2-Methyl-2,4-pentanediol
0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.366 α = 90 b = 26.929 β = 96.38 c = 63.532 γ = 90
Symmetry Space Group C 1 2 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 2024-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97915 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 2.54 31.57 95.34 0.095 0.061 0.994 6 6.7 3530 88.28
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 2.54 2.631 87.28 0.065 0.045 0.773 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8K0W 2.54 31.57 1.33 3397 181 95.34 0.22 0.218 0.2197 0.2751 0.2678 97.29
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 34.6576 f_angle_d 0.7078 f_chiral_restr 0.0334 f_bond_d 0.0049 f_plane_restr 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 669 Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing