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Structure of the adenine riboswitch aptamer domain in an intermediate-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 295 40 mM sodium cacodylate, pH 6.5, 80 mM potassium chloride, 100 mM magnesium chloride, 12 mM spermine tetrahydrochloride, 65% v/v (+/-)-2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.91 α = 90 b = 46.72 β = 94.06 c = 92.25 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL CS-PAD CXI-1 2016-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.3 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Split (All) 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 2.5 31.06 100 0.141 3.49 346.8 14357 80.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.8684 188.3 1431
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5E54 2.5 30.92 13212 768 97.62 0.1969 0.1949 0.2294 0.2609 RANDOM 90.59
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] -2.73 -0.58 2.41 0.4
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 5.272 r_angle_refined_deg 1.524 r_chiral_restr 0.101 r_gen_planes_refined 0.01 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2826 Solvent Atoms 15 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling PHASER phasing