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Crystal structure of Aromatic-amino-acid aminotransferase from Burkholderia pseudomallei covalently bound to pyridoxal phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EFF PDB ENTRY 4EFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Emerald Bio JCSG+ screen C1: 20% PEG8000, 100 mM phosphate/citrate, pH 4.2, 200 mM sodium chloride, 36.1 mg/mL BupsE.01471.a.A1 PW 34948 + 2.5 mM PLP, tray 233390c1, cryoprotectant: 10/20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.92 α = 90 b = 74.82 β = 90 c = 85.28 γ = 90
Symmetry Space Group P 21 21 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 CCD RIGAKU SATURN 944+ 2012-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.8 50 99.7 0.06 20.33 5 80697 80481 -3 22.744
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 1.8 1.85 98.7 0.465 2.47 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4EFF 1.8 50 80697 80427 4037 99.73 0.1625 0.1625 0.1607 0.1664 0.1964 0.1991 RANDOM 17.3325
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] -0.07 0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.77 r_dihedral_angle_4_deg 18.986 r_dihedral_angle_3_deg 12.879 r_dihedral_angle_1_deg 5.605 r_angle_refined_deg 1.586 r_angle_other_deg 0.963 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.77 r_dihedral_angle_4_deg 18.986 r_dihedral_angle_3_deg 12.879 r_dihedral_angle_1_deg 5.605 r_angle_refined_deg 1.586 r_angle_other_deg 0.963 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5996 Nucleic Acid Atoms Solvent Atoms 859 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection