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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 PDB 2PB2 PDB ENTRY 2PB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 293 1.4 M SODIUM MALONATE PH 7, 10% (V/V) MMT (MALATE-MES-TRIS) BUFFER AT PH 5.0, AT 293K WITH A PROTEIN TO CRYSTALLANT RATIO OF 3:1 IN THE PRESENCE OF SILVER BULLET SCREEN NUMBER 62.
Crystal Properties Matthews coefficient Solvent content 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 231.469 α = 90 b = 231.469 β = 90 c = 110.416 γ = 120
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 2011-04-12 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 2.75 19.9 99.3 0.15 21.9 22.1 29220 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 2.75 2.9 99.2 0.72 6 22.4
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 2PB2 2.75 115.73 27740 1480 99.17 0.15633 0.15398 0.1544 0.20133 0.1992 RANDOM 36.326
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] 1.83 0.91 1.83 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.271 r_dihedral_angle_4_deg 19.308 r_dihedral_angle_3_deg 18.201 r_dihedral_angle_1_deg 6.643 r_angle_refined_deg 1.803 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.271 r_dihedral_angle_4_deg 19.308 r_dihedral_angle_3_deg 18.201 r_dihedral_angle_1_deg 6.643 r_angle_refined_deg 1.803 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 5682 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing