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Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine
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, HANGING DROP 5.5 292 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350, 5mM gabaculine and 2mM PLP
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.258 α = 100.83 b = 60.887 β = 92.38 c = 63.499 γ = 107.86
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 2015-04-06 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 1.55 30 96.5 0.06 20.6 3.8 109959 16.7
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 1.55 1.58 94.7 0.55 3.2 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 1.55 30 104533 5425 95.68 0.15963 0.15805 0.19031 0.2209 RANDOM 23.099
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] -0.69 -1.88 -0.07 1.01 0.15 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.51 r_dihedral_angle_4_deg 18.879 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 5.513 r_long_range_B_other 5.359 r_scangle_other 1.831 r_angle_refined_deg 1.691 r_scbond_it 1.18 r_scbond_other 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.51 r_dihedral_angle_4_deg 18.879 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 5.953 r_long_range_B_refined 5.513 r_long_range_B_other 5.359 r_scangle_other 1.831 r_angle_refined_deg 1.691 r_scbond_it 1.18 r_scbond_other 1.18 r_mcangle_it 1.052 r_mcangle_other 1.052 r_angle_other_deg 1.024 r_mcbond_it 0.664 r_mcbond_other 0.661 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 6524 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 117
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 data collection HKL-3000 data scaling PHENIX phasing REFMAC refinement Coot model building HKL-3000 data reduction