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Co-crystal structure of the Geobacillus kaustophilus glyQ T-box riboswitch discriminator domain in complex with tRNA-Gly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 0.1 M Morpheus Buffer System 2 pH 7.5 (Sodium HEPES; MOPS (acid)), 0.09 M Halogens (NaF; NaBr; NaI), 10% w/v PEG 20000, and 20% v/v PEG 500 monomethyl ether (MME)
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.851 α = 90 b = 139.913 β = 90 c = 136.023 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 RAYONIX MX300-HS 2017-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.657 34.98 99.52 0.06249 0.06872 0.02815 0.998 16.89 6 12731 78.2675366044
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 2.657 2.752 97.59 1.152 1.263 0.5132 0.698 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.65703362888 34.97825 1.33790769823 12724 1263 99.5773986539 0.229497931299 0.224671142035 0.2317 0.272581164281 0.2746 89.1436737441
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 15.3829746504 f_angle_d 0.802318750364 f_chiral_restr 0.0345453769941 f_plane_restr 0.00477916731104 f_bond_d 0.00396829206797
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2755 Solvent Atoms 18 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling AutoSol phasing