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Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAT human Ornithine aminotransferase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG3350, 0.5M Ammonium acetate, 0.1M HEPES, 1mM Gabaculine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.065 α = 90 b = 111.966 β = 90 c = 65.489 γ = 90
Symmetry Space Group P 21 21 2
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 345 mm plate Osmic Mirrors 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.9 30 91.8 0.071 19 13.5 55871 51290 23.2
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 1.9 1.97 80.7 0.393 3.4 5525
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 human Ornithine aminotransferase 1.91 29.59 48704 2577 91.84 0.19774 0.19574 0.1931 0.23653 0.2342 RANDOM 20.319
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.551 r_dihedral_angle_4_deg 13.91 r_dihedral_angle_3_deg 13.337 r_dihedral_angle_1_deg 5.03 r_scangle_it 1.09 r_angle_refined_deg 0.93 r_scbond_it 0.668 r_mcangle_it 0.439 r_nbtor_refined 0.299 r_mcbond_it 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.551 r_dihedral_angle_4_deg 13.91 r_dihedral_angle_3_deg 13.337 r_dihedral_angle_1_deg 5.03 r_scangle_it 1.09 r_angle_refined_deg 0.93 r_scbond_it 0.668 r_mcangle_it 0.439 r_nbtor_refined 0.299 r_mcbond_it 0.258 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.143 r_xyhbond_nbd_refined 0.086 r_symmetry_hbond_refined 0.073 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5744 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing