3FVU | pdb_00003fvu

Crystal Structure of Human Kynurenine Aminotransferase I in Complex with Indole-3-acetic Acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W7L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529322% PEG 400, sodium acetate 0.2 M, Tris 0.1 M, 4% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2444.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.364α = 90
b = 108.454β = 114.2
c = 81.867γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
11.55300.0497.3122095
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)
11.551.610.523.86.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1W7L1.5529.22115737612099.760.185810.184510.180.210140.21RANDOM20.974
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]
0.030.010.03-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.737
r_dihedral_angle_4_deg16.407
r_dihedral_angle_3_deg12.887
r_dihedral_angle_1_deg8.398
r_scangle_it3.097
r_scbond_it1.967
r_angle_refined_deg1.33
r_mcangle_it1.259
r_mcbond_it0.697
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.737
r_dihedral_angle_4_deg16.407
r_dihedral_angle_3_deg12.887
r_dihedral_angle_1_deg8.398
r_scangle_it3.097
r_scbond_it1.967
r_angle_refined_deg1.33
r_mcangle_it1.259
r_mcbond_it0.697
r_nbtor_refined0.31
r_symmetry_vdw_refined0.201
r_nbd_refined0.199
r_metal_ion_refined0.149
r_symmetry_hbond_refined0.12
r_xyhbond_nbd_refined0.108
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms6738
Nucleic Acid Atoms
Solvent Atoms590
Heterogen Atoms58

Software

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