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Structures of inactive and activated DntR provide conclusive evidence for the mechanism of action of LysR transcription factors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UTB PDB ENTRY 1UTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2 M SODIUM TARTRATE, 0.2 M POTASSIUM THIOCYANATE 0.1 M TRIS-HCL PH 8.5, 20 % (W/V) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.57 65.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.472 α = 90 b = 107.472 β = 90 c = 297.771 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 6M BENT CYLINDRICAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 3.3 43.57 99.7 0.2 10.9 5.5 16127 -3 79.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.48 100 0.95 2.6 5.6
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 1UTB 3.3 43.57 1.36 16041 812 99.47 0.1908 0.1882 0.1923 0.2403 0.2415 76.2
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 14.439 f_angle_d 0.863 f_chiral_restr 0.058 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3332 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing