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Crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAA PDB ENTRY 1DAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 25% PEG4000, 0.2M Cacl2, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.6 α = 90 b = 73.98 β = 105.35 c = 76.21 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 IMAGE PLATE MAR scanner 300 mm plate 2013-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9798 APS 21-ID-F
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 50 99.6 0.045 19.8 3.74 39005 30.1
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 2.1 100 0.443 3.18 3.76 2863
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DAA 2.05 44.19 36949 1943 99.69 0.18141 0.17909 0.1875 0.22374 0.2297 RANDOM 36.062
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] 0.77 -0.19 0.05 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_4_deg 13.219 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 5.802 r_long_range_B_other 5.72 r_scangle_other 3.659 r_mcangle_it 2.914 r_mcangle_other 2.914 r_scbond_it 2.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_4_deg 13.219 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 5.802 r_long_range_B_other 5.72 r_scangle_other 3.659 r_mcangle_it 2.914 r_mcangle_other 2.914 r_scbond_it 2.404 r_scbond_other 2.404 r_mcbond_it 1.96 r_mcbond_other 1.959 r_angle_refined_deg 1.527 r_angle_other_deg 0.79 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4228 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 1
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling