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Crystal structure of 4-aminobutyrate transaminase from Mycobacterium smegmatis
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 6 290 Internal tracking number 216475B10. PACT screen condition B10:
0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG6000, MssmA.01026.b.A1 PW28765
at 25.2 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.22 α = 90 b = 98.41 β = 111.49 c = 109.61 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 CCD ADSC QUANTUM 315 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
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 2.05 19.76 93.8 0.082 10.24 3.27 106925 100299 -3 25.787
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 2.05 2.1 82.5 0.349 3.3 2.7 7879
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 3OKS 2.05 19.76 106925 100170 5025 93.9 0.195 0.195 0.193 0.2022 0.237 0.2464 RANDOM 18.659
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] 0.13 0.37 -0.51 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.959 r_dihedral_angle_4_deg 18.045 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 6.257 r_scangle_it 3.504 r_scbond_it 2.151 r_angle_refined_deg 1.476 r_mcangle_it 1.16 r_angle_other_deg 0.952 r_mcbond_it 0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.959 r_dihedral_angle_4_deg 18.045 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 6.257 r_scangle_it 3.504 r_scbond_it 2.151 r_angle_refined_deg 1.476 r_mcangle_it 1.16 r_angle_other_deg 0.952 r_mcbond_it 0.647 r_mcbond_other 0.179 r_chiral_restr 0.083 r_bond_refined_d 0.015 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 12772 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction