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YdaT transcription regulator (CII functional analog)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C4R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 ul 13.23 mg/ml YdaT (in 20mM Tris and 200mM NaCl, pH 7.5) mixed with 0.1 ul reservoir solution (0.1M BIS - TRIS pH 5.5, 2.0 M Ammonium sulphate) and equilibrated against 70 ul of reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.57 α = 66.83 b = 64.256 β = 89.36 c = 63.91 γ = 77.672
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 9M 2019-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.976 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.39 44.3725791252 77.3981758138 0.082 0.106 0.99 6 2.3325 19698 37.9536592773
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.52 0.386 0.552 0.797
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.39788433003 44.3725791252 1.97085360119 19687 979 77.3981758138 0.213955987448 0.211205561502 0.2109 0.265817898604 0.2677 56.1841727531
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 13.3314215494 f_angle_d 0.959225437611 f_chiral_restr 0.0549449884771 f_bond_d 0.00774529318575 f_plane_restr 0.00671038741088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3715 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing