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Unliganded structure of the ornithine aminotransferase from Toxoplasma gondii
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 5.5 290 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350, 0.5 mM oxidized glutathione
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.338 α = 100.88 b = 61.067 β = 92.23 c = 63.597 γ = 108.14
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 1.6 30 93.9 0.067 32.1 3.6 97272
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 1.6 1.63 92.5 0.46 2.86 3.5
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 1.6 30 92446 4794 93.2 0.178 0.177 0.183 0.214 0.2221 RANDOM 27.24
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] -1.79 -1.84 -0.64 2.3 0.8 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.64 r_dihedral_angle_4_deg 15.361 r_dihedral_angle_3_deg 10.131 r_long_range_B_refined 5.06 r_long_range_B_other 5.06 r_dihedral_angle_1_deg 3.483 r_scangle_other 2.309 r_angle_refined_deg 1.746 r_scbond_it 1.541 r_scbond_other 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.64 r_dihedral_angle_4_deg 15.361 r_dihedral_angle_3_deg 10.131 r_long_range_B_refined 5.06 r_long_range_B_other 5.06 r_dihedral_angle_1_deg 3.483 r_scangle_other 2.309 r_angle_refined_deg 1.746 r_scbond_it 1.541 r_scbond_other 1.54 r_mcangle_it 1.426 r_mcangle_other 1.426 r_angle_other_deg 0.949 r_mcbond_it 0.942 r_mcbond_other 0.94 r_chiral_restr 0.115 r_gen_planes_refined 0.025 r_gen_planes_other 0.019 r_bond_refined_d 0.014 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 6535 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing Coot model building