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Crystal structure of a putative ornithine aminotransferase from Toxoplasma gondii ME49 in complex with pyrodoxal-5'-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LG0 PDB ENTRY 3LG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium Acetate, 0.1 M Bis-Tris, 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.19 α = 100.58 b = 61.328 β = 93.23 c = 63.678 γ = 107.74
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 beryllium lenses 2013-10-31 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 1.2 62.14 91 0.043 11.2 2 224574 224574 -3 14.4
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 1.2 1.22 91 0.37 2 2 11241
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3LG0 1.2 62.14 213305 213305 11260 90.85 0.13481 0.13322 0.16494 0.1936 RANDOM 18.365
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] 0.29 -0.59 0.58 0.01 1.34 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.552 r_sphericity_bonded 27.542 r_rigid_bond_restr 25.184 r_sphericity_free 24.018 r_dihedral_angle_4_deg 17.237 r_dihedral_angle_3_deg 12.555 r_scangle_other 10.775 r_scbond_it 10.55 r_scbond_other 10.55 r_long_range_B_other 8.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.552 r_sphericity_bonded 27.542 r_rigid_bond_restr 25.184 r_sphericity_free 24.018 r_dihedral_angle_4_deg 17.237 r_dihedral_angle_3_deg 12.555 r_scangle_other 10.775 r_scbond_it 10.55 r_scbond_other 10.55 r_long_range_B_other 8.96 r_long_range_B_refined 8.777 r_dihedral_angle_1_deg 6.07 r_mcangle_other 5.581 r_mcangle_it 5.577 r_mcbond_it 4.662 r_mcbond_other 4.66 r_angle_refined_deg 1.927 r_angle_other_deg 0.966 r_chiral_restr 0.152 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6560 Nucleic Acid Atoms Solvent Atoms 1041 Heterogen Atoms 65
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling