5E3K

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1141.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.328α = 100.72
b = 61.524β = 92.96
c = 63.555γ = 108.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97913APS21-ID-D

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
11.73097.30.0620.9384366
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)
11.71.7395.70.51.92.4

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 REPLACEMENTTHROUGHOUT4NOG1.73080138422896.410.15590.153740.19601RANDOM22.798
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]
-0.95-1.64-0.831.04-0.51.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.945
r_dihedral_angle_4_deg18.739
r_dihedral_angle_3_deg12.598
r_dihedral_angle_1_deg6.34
r_long_range_B_refined5.467
r_long_range_B_other5.467
r_scangle_other1.807
r_angle_refined_deg1.749
r_scbond_it1.182
r_scbond_other1.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.945
r_dihedral_angle_4_deg18.739
r_dihedral_angle_3_deg12.598
r_dihedral_angle_1_deg6.34
r_long_range_B_refined5.467
r_long_range_B_other5.467
r_scangle_other1.807
r_angle_refined_deg1.749
r_scbond_it1.182
r_scbond_other1.182
r_angle_other_deg1.041
r_mcangle_it1.039
r_mcangle_other1.038
r_mcbond_it0.672
r_mcbond_other0.672
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms6560
Nucleic Acid Atoms
Solvent Atoms813
Heterogen Atoms114

Software

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