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Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.481 α = 100.45 b = 61.459 β = 92.39 c = 63.435 γ = 108.32
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 1.8 30 96 0.03 22.1 1.8 70729 70729
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 1.8 1.83 87.4 0.46 1.5 1.7
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 4NGO 1.8 30 67239 3490 95.69 0.16408 0.16191 0.1698 0.20591 0.2131 RANDOM 35.798
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] 0.01 -2.64 -0.62 1.29 -0.53 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.109 r_dihedral_angle_4_deg 17.303 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 6.321 r_long_range_B_refined 5.727 r_long_range_B_other 5.675 r_scangle_other 1.716 r_angle_refined_deg 1.628 r_mcangle_it 1.225 r_mcangle_other 1.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.109 r_dihedral_angle_4_deg 17.303 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 6.321 r_long_range_B_refined 5.727 r_long_range_B_other 5.675 r_scangle_other 1.716 r_angle_refined_deg 1.628 r_mcangle_it 1.225 r_mcangle_other 1.225 r_scbond_it 1.131 r_scbond_other 1.123 r_angle_other_deg 1 r_mcbond_it 0.757 r_mcbond_other 0.757 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 6533 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 67
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 phasing HKL-3000 data scaling PHASER phasing REFMAC refinement HKL-3000 data reduction