5EQC

Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of PLP at the protein active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NOG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Na Thiocyanate, 20% PEG3350, 0.5 mM oxidized glutathione
Crystal Properties
Matthews coefficientSolvent content
3.463.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.406α = 90
b = 109.406β = 90
c = 109.883γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2301000.1123.48.365316
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.241000.73.38.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NOG2.2306206332191000.1460.1450.181RANDOM37.35
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]
-1.09-1.092.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.214
r_dihedral_angle_4_deg17.872
r_dihedral_angle_3_deg14.75
r_dihedral_angle_1_deg6.224
r_long_range_B_refined6.099
r_long_range_B_other6.099
r_scangle_other3.51
r_scbond_it2.29
r_scbond_other2.29
r_mcangle_it1.988
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.214
r_dihedral_angle_4_deg17.872
r_dihedral_angle_3_deg14.75
r_dihedral_angle_1_deg6.224
r_long_range_B_refined6.099
r_long_range_B_other6.099
r_scangle_other3.51
r_scbond_it2.29
r_scbond_other2.29
r_mcangle_it1.988
r_mcangle_other1.988
r_angle_refined_deg1.915
r_mcbond_it1.235
r_mcbond_other1.234
r_angle_other_deg1.067
r_chiral_restr0.131
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms6579
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing