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Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 0.1 M NaCacodylate pH 7.1, PEG3350 16%, 0.25 M Magnesium Acetate
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.27 α = 90 b = 53.27 β = 90 c = 188.036 γ = 90
Symmetry Space Group I 41 2 2
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 PILATUS3 6M 2018-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.51 40.59 99.9 0.05 20.9 10.2 20010 23.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.61 98.6 1 1.5 10.6
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 6E8S 1.55 40.59 1.36 20010 1856 98.65 0.1794 0.1767 0.1804 0.2064 0.2109 32.67
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 22.0348 f_angle_d 1.1228 f_chiral_restr 0.0473 f_plane_restr 0.0111 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 788 Solvent Atoms 143 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing