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Structural and functional study of succinyl-ornithine transaminase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PREVIOUSLY-DETERMINED NATIVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 293 1.5 M AMMONIUM SULFATE, 10% (V/V) MMT (MALATE-MES-TRIS) BUFFER AT PH 9.0, 293K, 150 PLUS 150 NL DROPS. PROTEIN HAD PLP AND SUCCINYLORNITHINE PREVIOUSLY ADDED.
Crystal Properties Matthews coefficient Solvent content 3.43 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.938 α = 90 b = 118.264 β = 96.82 c = 109.238 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 CCD ADSC QUANTUM 315 2011-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 2.45 19.8 99.8 0.15 10.6 5.9 85143 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 2.45 2.58 100 0.63 2.9 5.9
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 PREVIOUSLY-DETERMINED NATIVE 2.45 108.46 80886 4254 99.77 0.17303 0.17026 0.1719 0.22534 0.2271 RANDOM 28.142
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] -1.36 0.62 3.52 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.408 r_dihedral_angle_4_deg 20.644 r_dihedral_angle_3_deg 19.439 r_dihedral_angle_1_deg 7.172 r_angle_refined_deg 2.095 r_chiral_restr 0.145 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.408 r_dihedral_angle_4_deg 20.644 r_dihedral_angle_3_deg 19.439 r_dihedral_angle_1_deg 7.172 r_angle_refined_deg 2.095 r_chiral_restr 0.145 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12144 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing