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Ligand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TZX
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 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.9 α = 90 b = 154.9 β = 90 c = 25.2 γ = 90
Symmetry Space Group P 21 21 2
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 3 26.32 95 0.6689 1.37 20.3 4115 66.4
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 3 3.31 87 1.0157 13 945
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4TZX 3 26.32 3919 196 94.93 0.3503 0.3489 0.3471 0.379 0.3756 RANDOM 58.062
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] 4.32 -2.91 -1.41
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 1.91 r_angle_refined_deg 0.856 r_chiral_restr 0.07 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1502 Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling PHASER phasing