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structure of ydao riboswitch binding with c-di-dAMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 0.1 M Na-Bicine, pH 8.7-9.2 and 2.6-3.2 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 59.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.874 α = 90 b = 87.051 β = 90 c = 144.553 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 50 1 49287 1.1
Refinement Statistics Diffraction ID Structure Solution 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 2.65 45.25 1.34 13780 732 99.4 0.221 0.217 0.2295 0.29 0.2974
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 24.397 f_angle_d 1.82 f_chiral_restr 0.166 f_bond_d 0.015 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2514 Solvent Atoms 7 Heterogen Atoms 86
Software Software Software Name Purpose XDS data scaling PHASER phasing PHENIX refinement XDS data reduction