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Crystal structure of a 4-aminobutyrate aminotransferase (GabT) from Mycobacterium abscessus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKS pdb entry 3oks
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 MyabA.01026.b.A1 PS00899 at 20 mg/mL against PACT F6 0.2 M sodium formate, 0.1 M Bis Tris Propane pH 6.5, 20% PEG 3350, crystal tracking ID 233334f6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.4 α = 78.06 b = 67.53 β = 81.26 c = 102.46 γ = 77.44
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+ VariMax 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 96.2 0.038 29.14 5.2 158993 152966 -3 19.198
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 85.9 0.123 8.03
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 pdb entry 3oks 1.8 50 145353 7697 96.3 0.1396 0.1381 0.1669 0.1635 RANDOM 12.6276
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] 0.44 -0.39 0.2 -0.02 -0.09 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 15.096 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_1_deg 5.715 r_angle_refined_deg 1.392 r_angle_other_deg 0.931 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.145 r_dihedral_angle_4_deg 15.096 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_1_deg 5.715 r_angle_refined_deg 1.392 r_angle_other_deg 0.931 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12901 Nucleic Acid Atoms Solvent Atoms 1912 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction