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Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L0U PDB ENTRIES 3L0U and 3V7E experimental model PDB 3V7E PDB ENTRIES 3L0U and 3V7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 50 mM Bis-Tris (HCl) pH 6.5, 300 mM Li2SO4, and 20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.382 α = 90 b = 108.474 β = 90 c = 266.886 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 CCD ADSC QUANTUM 315 2012-08-02 M SINGLE WAVELENGTH 2 1 CCD ADSC QUANTUM 315 3 1 CCD ADSC QUANTUM 315r 4 1 CCD ADSC QUANTUM 315r
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9793 APS 24-ID-E 2 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9793 APS 24-ID-C 3 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9793 ALS 5.0.1 4 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9793 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.2 28.42 98.9 0.062 11.1 6.1 1.5 1.5 128.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.2653 98
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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, SAD PDB ENTRIES 3L0U and 3V7E 3.2 28.416 1.34 46354 45770 2318 98.74 0.1984 0.1957 0.1969 0.2514 0.2495 Random 128.0007
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 15.422 f_angle_d 0.366 f_chiral_restr 0.02 f_bond_d 0.001 f_plane_restr 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1048 Nucleic Acid Atoms 7586 Solvent Atoms 22 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction XDS data scaling SHELXD phasing PHENIX phasing