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Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid
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 6.5 293 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.328 α = 100.72 b = 61.524 β = 92.96 c = 63.555 γ = 108.18
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 2015-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97913 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 97.3 0.06 20.9 3 84366
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 95.7 0.5 1.9 2.4
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 4NOG 1.7 30 80138 4228 96.41 0.1559 0.15374 0.1663 0.19601 0.2033 RANDOM 22.798
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] -0.95 -1.64 -0.83 1.04 -0.5 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.945 r_dihedral_angle_4_deg 18.739 r_dihedral_angle_3_deg 12.598 r_dihedral_angle_1_deg 6.34 r_long_range_B_refined 5.467 r_long_range_B_other 5.467 r_scangle_other 1.807 r_angle_refined_deg 1.749 r_scbond_it 1.182 r_scbond_other 1.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.945 r_dihedral_angle_4_deg 18.739 r_dihedral_angle_3_deg 12.598 r_dihedral_angle_1_deg 6.34 r_long_range_B_refined 5.467 r_long_range_B_other 5.467 r_scangle_other 1.807 r_angle_refined_deg 1.749 r_scbond_it 1.182 r_scbond_other 1.182 r_angle_other_deg 1.041 r_mcangle_it 1.039 r_mcangle_other 1.038 r_mcbond_it 0.672 r_mcbond_other 0.672 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 6560 Nucleic Acid Atoms Solvent Atoms 813 Heterogen Atoms 114
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 data scaling PHASER phasing Coot model building REFMAC refinement HKL-3000 data reduction