3AOV

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PLP


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 magnesium chloride hexahydrate, 0.1M HEPES sodium pH7.5, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.927α = 90
b = 71.055β = 89.99
c = 136.348γ = 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
11.725099.20.0710.06331.67.586393
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)
11.721000.5670.4152.757.54357

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 1X0M1.7226.8482018433398.890.186110.183710.23156RANDOM30.879
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]
-2.21-0.113.29-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.151
r_dihedral_angle_4_deg20.597
r_dihedral_angle_3_deg14.884
r_dihedral_angle_1_deg6.774
r_scangle_it5.634
r_scbond_it3.461
r_mcangle_it2.315
r_angle_refined_deg2.121
r_mcbond_it1.397
r_chiral_restr0.151
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.151
r_dihedral_angle_4_deg20.597
r_dihedral_angle_3_deg14.884
r_dihedral_angle_1_deg6.774
r_scangle_it5.634
r_scbond_it3.461
r_mcangle_it2.315
r_angle_refined_deg2.121
r_mcbond_it1.397
r_chiral_restr0.151
r_bond_refined_d0.026
r_gen_planes_refined0.013
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 Atoms585
Heterogen Atoms30

Software

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