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2.3 A resolution crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49
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 5.5 293 0.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.418 α = 100.7 b = 60.804 β = 92.63 c = 63.379 γ = 107.68
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 0.9788 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 2.3 30 96.9 0.07 15.7 2 33287 33287
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 2.3 2.34 97.2 0.49 2.2 1.9
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 2.31 30 31691 1595 96.27 0.1899 0.18639 0.25848 0.2451 RANDOM 33.965
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] 0.8 -1.02 -0.77 0.16 -1.28 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.704 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 15.212 r_dihedral_angle_1_deg 6.669 r_long_range_B_refined 3.253 r_long_range_B_other 3.193 r_angle_refined_deg 1.561 r_scangle_other 1.518 r_mcangle_it 1.406 r_mcangle_other 1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.704 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 15.212 r_dihedral_angle_1_deg 6.669 r_long_range_B_refined 3.253 r_long_range_B_other 3.193 r_angle_refined_deg 1.561 r_scangle_other 1.518 r_mcangle_it 1.406 r_mcangle_other 1.406 r_scbond_it 1.255 r_angle_other_deg 0.98 r_scbond_other 0.898 r_mcbond_it 0.821 r_mcbond_other 0.82 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 6546 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 90
Software Software Software Name Purpose BLU-MAX data collection HKL-2000 data scaling PHASER phasing REFMAC refinement HKL-2000 data reduction