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Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 50 mM MES, pH 5.6, 10 mM MgCl2, 1.8 M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.89 57.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.158 α = 90 b = 118.442 β = 90 c = 119.31 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 PILATUS 6M-F 2017-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.86 80.27 99.15 0.06 0.062 0.017 1 21.6 12.9 63989 41.9006599711
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.91 94.9 2.3 2.405 0.685 0.476 0.9 11.5
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 4ZKE 1.86541345549 37.59 1.33645911288 63984 3857 99.1452236156 0.219691816645 0.219263394781 0.2219 0.233109193783 0.238 52.6096131687
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 16.7204883617 f_angle_d 0.740218111377 f_chiral_restr 0.0419224614266 f_plane_restr 0.00486278714805 f_bond_d 0.00379780219267
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3295 Nucleic Acid Atoms 1286 Solvent Atoms 252 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX phasing