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The first crystal structure of the DABA aminotransferase EctB in the ectoine biosynthesis pathway of the model organism Chromohalobacter salexigens DSM 3034
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2M sodium malonate,
0.1M BisTris propane pH 6.5,
30% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.055 α = 90 b = 124.782 β = 98.95 c = 145.416 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M toroidal mirror 2018-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.99187 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.45 49.073 98.9 0.047 10.6 3.4 136967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 99.6 1.07 0.7 3.4
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 1sf2 2.45 49.073 1.33 136907 2703 98.79 0.1861 0.1849 0.1869 0.2435 0.2418
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 4.09 f_angle_d 0.998 f_chiral_restr 0.055 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25722 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 120
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing Coot model building PHENIX refinement