☰ Navigation Tabs
Cocrystal Structure of the Nocardia farcinica ileS T-box riboswitch in complex with its cognate tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LCK tRNA-Gly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 20-25 % PEG 3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M Li2SO4, 10 mM MgCl2, 1 mM Spermine
Crystal Properties Matthews coefficient Solvent content 3.15 60.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.23 α = 90 b = 93.98 β = 90 c = 179.63 γ = 90
Symmetry Space Group P 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 PIXEL DECTRIS EIGER X 16M 2018-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.82 46.99 99.3 0.08 0.994 15.2 13 17899 92.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.92 99.4 1.96 0.712 1.2 10.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 SAD FREE R-VALUE tRNA-Gly 2.82 46.99 1.34 33032 3311 99.22 0.195 0.1907 0.1994 0.2327 0.2478 142.52
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 16.5379 f_angle_d 0.7416 f_chiral_restr 0.0374 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3754 Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose SERGUI data collection XDS data reduction XSCALE data scaling PHASER phasing AutoSol phasing Coot model building PHENIX refinement