4NOG

Crystal structure of a putative ornithine aminotransferase from Toxoplasma gondii ME49 in complex with pyrodoxal-5'-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LG0PDB ENTRY 3LG0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Ammonium Acetate, 0.1 M Bis-Tris, 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.19α = 100.58
b = 61.328β = 93.23
c = 63.678γ = 107.74
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2013-10-31MSINGLE 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
11.262.14910.04311.22224574224574-314.4
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)
11.21.22910.372211241

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3LG01.262.142133052133051126090.850.134810.133220.16494RANDOM18.365
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]
0.29-0.590.580.011.34-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.552
r_sphericity_bonded27.542
r_rigid_bond_restr25.184
r_sphericity_free24.018
r_dihedral_angle_4_deg17.237
r_dihedral_angle_3_deg12.555
r_scangle_other10.775
r_scbond_it10.55
r_scbond_other10.55
r_long_range_B_other8.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.552
r_sphericity_bonded27.542
r_rigid_bond_restr25.184
r_sphericity_free24.018
r_dihedral_angle_4_deg17.237
r_dihedral_angle_3_deg12.555
r_scangle_other10.775
r_scbond_it10.55
r_scbond_other10.55
r_long_range_B_other8.96
r_long_range_B_refined8.777
r_dihedral_angle_1_deg6.07
r_mcangle_other5.581
r_mcangle_it5.577
r_mcbond_it4.662
r_mcbond_other4.66
r_angle_refined_deg1.927
r_angle_other_deg0.966
r_chiral_restr0.152
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6560
Nucleic Acid Atoms
Solvent Atoms1041
Heterogen Atoms65

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling