3E2F | pdb_00003e2f

Crystal structure of mouse kynurenine aminotransferase III, PLP-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZJGPDB entry 2ZJG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527721% PEG 400, 150 mM CaCl2, 10% Glycerol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3948.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.82α = 90
b = 91.82β = 90
c = 233.649γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2008-06-27MSINGLE 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
12.593091.10.1510.43202329301
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)
12.592.690.522

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 REPLACEMENTTHROUGHOUTPDB entry 2ZJG2.5929.21275931476910.195850.193270.190.246430.24RANDOM30.531
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.139
r_dihedral_angle_3_deg21.047
r_dihedral_angle_4_deg20.706
r_dihedral_angle_1_deg10.202
r_scangle_it5.141
r_scbond_it3.44
r_angle_refined_deg2.211
r_mcangle_it2.155
r_mcbond_it1.168
r_nbtor_refined0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.139
r_dihedral_angle_3_deg21.047
r_dihedral_angle_4_deg20.706
r_dihedral_angle_1_deg10.202
r_scangle_it5.141
r_scbond_it3.44
r_angle_refined_deg2.211
r_mcangle_it2.155
r_mcbond_it1.168
r_nbtor_refined0.34
r_symmetry_vdw_refined0.302
r_symmetry_hbond_refined0.282
r_chiral_restr0.278
r_nbd_refined0.273
r_xyhbond_nbd_refined0.183
r_bond_refined_d0.025
r_gen_planes_refined0.011
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_refined
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 Atoms6536
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms60

Software

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