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Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3-Biotin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1 M HEPES pH 7.5, 2.45 M Ammonium Formate, 12.5% glycerol, 3% sorbitol
Crystal Properties Matthews coefficient Solvent content 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.098 α = 90 b = 181.764 β = 90 c = 108.289 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M 2017-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9762 ALS 5.0.1
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 3 46.52 99.8 0.098 4.3 10.5 7735 58.7167495741
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 3 3.19 99.6 0.93 0.5 4.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6C63 3.00014879601 46.5151662692 1.34562114754 7735 776 99.7421018698 0.196349464513 0.189856262024 0.1976 0.255076205615 0.2587 random selection 57.3830391657
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 21.5244344709 f_angle_d 1.19961570462 f_chiral_restr 0.0538579029803 f_plane_restr 0.00710507899163 f_bond_d 0.00575984244903
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2281 Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing