4ZWM

2.3 A resolution crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2 M AmmSO4, 0.1 M Bis-Tris, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0941.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.418α = 100.7
b = 60.804β = 92.63
c = 63.379γ = 107.68
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-D0.9788APS21-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
12.33096.90.0715.723328733287
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)
12.32.3497.20.492.21.9

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 REPLACEMENTTHROUGHOUT4NOG2.313031691159596.270.18990.186390.25848RANDOM33.965
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]
0.8-1.02-0.770.16-1.280.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.704
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg15.212
r_dihedral_angle_1_deg6.669
r_long_range_B_refined3.253
r_long_range_B_other3.193
r_angle_refined_deg1.561
r_scangle_other1.518
r_mcangle_it1.406
r_mcangle_other1.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.704
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg15.212
r_dihedral_angle_1_deg6.669
r_long_range_B_refined3.253
r_long_range_B_other3.193
r_angle_refined_deg1.561
r_scangle_other1.518
r_mcangle_it1.406
r_mcangle_other1.406
r_scbond_it1.255
r_angle_other_deg0.98
r_scbond_other0.898
r_mcbond_it0.821
r_mcbond_other0.82
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms6546
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms90

Software

Software
Software NamePurpose
BLU-MAXdata collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction