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Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to 7-keto 8-amino pelargonic acid (KAPA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A0F PDB ENTRY 4A0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M AMMONIUM TARTRATE PH 6.2, 15 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 235.32 α = 90 b = 76.94 β = 109.89 c = 89.22 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.81 44.57 99 0.11 9.22 3.78 36581 -3 52.68
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 2.81 2.88 91.5 0.65 1.61 1.74
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 4A0F 2.808 44.572 1.99 36557 1822 99.1 0.197 0.1934 0.1848 0.2619 0.2555 66.7
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] -11.072 5.2037 19.4404 -8.3684
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.345 f_angle_d 1.354 f_chiral_restr 0.08 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11346 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing