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Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Na Thiocyanate, 20% PEG3350, 0.5 mM oxidized glutathione
Crystal Properties Matthews coefficient Solvent content 3.4 63.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.406 α = 90 b = 109.406 β = 90 c = 109.883 γ = 90
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 MARMOSAIC 225 mm CCD 2015-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 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 2.2 30 100 0.11 23.4 8.3 65316
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 2.2 2.24 100 0.7 3.3 8.2
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 4NOG 2.2 30 62063 3219 100 0.146 0.145 0.152 0.181 0.1856 RANDOM 37.35
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] -1.09 -1.09 2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.214 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_1_deg 6.224 r_long_range_B_refined 6.099 r_long_range_B_other 6.099 r_scangle_other 3.51 r_scbond_it 2.29 r_scbond_other 2.29 r_mcangle_it 1.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.214 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_1_deg 6.224 r_long_range_B_refined 6.099 r_long_range_B_other 6.099 r_scangle_other 3.51 r_scbond_it 2.29 r_scbond_other 2.29 r_mcangle_it 1.988 r_mcangle_other 1.988 r_angle_refined_deg 1.915 r_mcbond_it 1.235 r_mcbond_other 1.234 r_angle_other_deg 1.067 r_chiral_restr 0.131 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6579 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing