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Crystal structure of 4-aminobutyrate aminotransferase GabT from Mycobacterium marinum covalently bound to pyridoxal phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MymaA.01026.b.A1 PW29968 at 27.8 mg/mL against JCSG+ screen condition D5, 70% MPD, 0.1 M Hepes pH 7.5, crystal tracking ID 220563d5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.49 64.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.62 α = 90 b = 123.62 β = 90 c = 157.59 γ = 120
Symmetry Space Group P 62 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 CCD ADSC QUANTUM 315r 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 2.5 50 100 0.118 15.33 8.9 26253 25245 -3 37.813
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 2.5 2.57 100 0.559 3.74 9.1 1834
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3oks 2.5 50 25110 1281 99.46 0.1533 0.1513 0.191 0.1636 RANDOM 28.8302
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] 0.94 0.47 0.94 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 6.106 r_scangle_it 3.874 r_scbond_it 2.267 r_angle_refined_deg 1.453 r_mcangle_it 1.107 r_mcbond_it 0.541 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 6.106 r_scangle_it 3.874 r_scbond_it 2.267 r_angle_refined_deg 1.453 r_mcangle_it 1.107 r_mcbond_it 0.541 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3293 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction