3AV7

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, KYN as substrates and KYA as products


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AOVPDB ENTRY 3AOV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82770.1M imidazole pH 8.0, 0.2M calcium acetate, 20% w/v polyethylene glycol 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.619α = 90
b = 136.529β = 100.71
c = 55.612γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2010-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11SPring-8BL38B1

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
11.844093.30.0813.567298
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)
11.851.8896.70.6531.493.5

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 3AOV1.8426.6963854341195.70.179290.176180.2379RANDOM30.47
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]
0.52.2-0.020.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.318
r_dihedral_angle_4_deg20.885
r_dihedral_angle_3_deg15.559
r_dihedral_angle_1_deg6.907
r_scangle_it5.424
r_scbond_it3.447
r_mcangle_it2.051
r_angle_refined_deg2.019
r_mcbond_it1.207
r_chiral_restr0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.318
r_dihedral_angle_4_deg20.885
r_dihedral_angle_3_deg15.559
r_dihedral_angle_1_deg6.907
r_scangle_it5.424
r_scbond_it3.447
r_mcangle_it2.051
r_angle_refined_deg2.019
r_mcbond_it1.207
r_chiral_restr0.147
r_bond_refined_d0.025
r_gen_planes_refined0.011
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 Atoms555
Heterogen Atoms90

Software

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