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PRPP riboswitch from T. mathranii bound to PRPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T83 PDB entry 5T83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.6 303.15 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 10 mM PRPP, mixed 2:1 with 80 mM sodium chloride, 20 mM barium chloride dihydrate, 40 mM sodium cacodylate trihydrate, pH 5.6, 45% v/v MPD, 12 mM spermine tetrahydrachloride. Crystals were flash-frozen without further preparation.
Crystal Properties Matthews coefficient Solvent content 2.73 54.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.977 α = 90 b = 89.575 β = 96.9 c = 136.367 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 100 PIXEL DECTRIS EIGER X 16M 2017-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (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 40 98.2 0.1 0.118 0.061 9.3 3.6 27959
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 2.5 2.54 98.9 1.068 1.246 0.633 0.176 3.9
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 PDB entry 5T83 2.49 37.35 26309 1361 96.98 0.2164 0.2145 0.2144 0.2523 0.25 RANDOM 78.592
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] 51.63 -31.18 8.9 -60.53
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.842 r_angle_other_deg 1.769 r_chiral_restr 0.115 r_gen_planes_refined 0.014 r_bond_refined_d 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 4418 Solvent Atoms 52 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing SCALEPACK data scaling Coot model building HKL-2000 data reduction