3AOW

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with AKG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X0MPDB ENTRY 1X0M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2M calcium chloride dehydrate, 0.1M HEPES sodium pH7.5, 28% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.774α = 90
b = 70.977β = 89.99
c = 136.723γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2010-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.9SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.565099.50.0540.04125.73.8115232
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5793.70.6920.51.573.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1X0M1.5626.81109393578099.460.179650.17730.22391RANDOM25.502
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]
-1.560.212.36-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg21.068
r_dihedral_angle_3_deg14.911
r_dihedral_angle_1_deg6.789
r_scangle_it5.99
r_scbond_it3.684
r_mcangle_it2.43
r_angle_refined_deg2.366
r_mcbond_it1.46
r_chiral_restr0.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg21.068
r_dihedral_angle_3_deg14.911
r_dihedral_angle_1_deg6.789
r_scangle_it5.99
r_scbond_it3.684
r_mcangle_it2.43
r_angle_refined_deg2.366
r_mcbond_it1.46
r_chiral_restr0.178
r_bond_refined_d0.028
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6494
Nucleic Acid Atoms
Solvent Atoms838
Heterogen Atoms50

Software

Software
Software NamePurpose
BL38B1data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling