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Structure of the ornithine aminotransferase from Toxoplasma gondii in complex with inactivator
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 6.5 291 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.408 α = 100.87 b = 61.445 β = 92.48 c = 63.665 γ = 108.12
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 300 mm CCD 2015-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97889 APS 21-ID-D
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 1.7 30 92.6 0.054 35.4 3.8 81340 81340
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 1.7 1.73 95.6 0.67 2.06 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4NOG 1.7 30 77255 4073 92.39 0.17054 0.16849 0.20784 0.2223 RANDOM 31.953
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] -0.52 -1.11 -0.41 2.29 -1.79 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.568 r_dihedral_angle_4_deg 14.362 r_dihedral_angle_3_deg 10.697 r_long_range_B_refined 5.328 r_long_range_B_other 5.286 r_dihedral_angle_1_deg 3.418 r_scangle_other 2.659 r_angle_refined_deg 1.844 r_scbond_it 1.805 r_scbond_other 1.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.568 r_dihedral_angle_4_deg 14.362 r_dihedral_angle_3_deg 10.697 r_long_range_B_refined 5.328 r_long_range_B_other 5.286 r_dihedral_angle_1_deg 3.418 r_scangle_other 2.659 r_angle_refined_deg 1.844 r_scbond_it 1.805 r_scbond_other 1.804 r_mcangle_it 1.542 r_mcangle_other 1.542 r_mcbond_it 1.124 r_mcbond_other 1.124 r_angle_other_deg 0.992 r_chiral_restr 0.119 r_gen_planes_refined 0.026 r_gen_planes_other 0.02 r_bond_refined_d 0.015 r_bond_other_d 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 6524 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 95
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 data collection HKL-3000 data scaling PHASER phasing REFMAC refinement Coot model building HKL-3000 data reduction