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TtgR in complex with resveratrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 nL of protein at 9.8 mg/mL (0.41 millimolar) in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP and 0.5 millimolar resveratrol was equilibrated against 250 nL 18% PEG4000, 0.2M MgCl2, 0.1M bistris HCl pH 6.5 in a SD2 plate using a Mosquito crystallization robot. Samples were cryoprotected with reservoir solution supplemented with 35% PEG4000. Samples looped in Mitegen micro mounts were flash cooled by immersion in liquid nitrogen. Crystals were grown at 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.73 α = 90 b = 64.5 β = 90 c = 223.22 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 MARMOSAIC 300 mm CCD 3.0 Undulator C(111) monochromator 2018-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978560 APS 21-ID-G
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 1.9 28.63 99.88 0.07704 0.07997 0.02123 0.999 22.92 14.4 33367 36.4
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 1.9 1.968 99.97 1.294 1.339 0.3446 0.739 2.06 14.9
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 MOLECULAR REPLACEMENT FREE R-VALUE 2XDN 1.9 28.63 1.36 33349 2020 99.92 0.1859 0.1834 0.1854 0.2247 0.2267 42.83
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 14.6113 f_angle_d 1.2254 f_chiral_restr 0.0607 f_bond_d 0.016 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3295 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing