4ZLV

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52940.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1141.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.481α = 100.45
b = 61.459β = 92.39
c = 63.435γ = 108.32
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97889APS21-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
11.830960.0322.11.87072970729
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)
11.81.8387.40.461.51.7

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 REPLACEMENTTHROUGHOUT4NGO1.83067239349095.690.164080.161910.20591RANDOM35.798
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]
0.01-2.64-0.621.29-0.530.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.109
r_dihedral_angle_4_deg17.303
r_dihedral_angle_3_deg13.143
r_dihedral_angle_1_deg6.321
r_long_range_B_refined5.727
r_long_range_B_other5.675
r_scangle_other1.716
r_angle_refined_deg1.628
r_mcangle_it1.225
r_mcangle_other1.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.109
r_dihedral_angle_4_deg17.303
r_dihedral_angle_3_deg13.143
r_dihedral_angle_1_deg6.321
r_long_range_B_refined5.727
r_long_range_B_other5.675
r_scangle_other1.716
r_angle_refined_deg1.628
r_mcangle_it1.225
r_mcangle_other1.225
r_scbond_it1.131
r_scbond_other1.123
r_angle_other_deg1
r_mcbond_it0.757
r_mcbond_other0.757
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms6533
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms67

Software

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