5DJ9

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52920.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350, 5mM gabaculine and 2mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.0941.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.258α = 100.83
b = 60.887β = 92.38
c = 63.499γ = 107.86
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-06MSINGLE 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
11.553096.50.0620.63.810995916.7
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)
11.551.5894.70.553.23.8

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 REPLACEMENTTHROUGHOUT4NOG1.5530104533542595.680.159630.158050.19031RANDOM23.099
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]
-0.69-1.88-0.071.010.150.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.51
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg12.519
r_dihedral_angle_1_deg5.953
r_long_range_B_refined5.513
r_long_range_B_other5.359
r_scangle_other1.831
r_angle_refined_deg1.691
r_scbond_it1.18
r_scbond_other1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.51
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg12.519
r_dihedral_angle_1_deg5.953
r_long_range_B_refined5.513
r_long_range_B_other5.359
r_scangle_other1.831
r_angle_refined_deg1.691
r_scbond_it1.18
r_scbond_other1.18
r_mcangle_it1.052
r_mcangle_other1.052
r_angle_other_deg1.024
r_mcbond_it0.664
r_mcbond_other0.661
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms6524
Nucleic Acid Atoms
Solvent Atoms726
Heterogen Atoms117

Software

Software
Software NamePurpose
BLU-MAXdata collection
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction