1W7N

Crystal structure of human kynurenine aminotransferase I in PMP form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W7LPDB ENTRY 1W7L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7.00
Crystal Properties
Matthews coefficientSolvent content
4.2771.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.461α = 90
b = 145.461β = 90
c = 67.087γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMSCMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
12.93099.30.16.118243

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 1W7L2.938.92176625641000.1720.1710.22RANDOM50.84
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]
-4.15-2.07-4.156.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.975
r_scangle_it3.923
r_scbond_it2.235
r_angle_refined_deg1.66
r_mcangle_it1.571
r_mcbond_it0.801
r_nbd_refined0.241
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.975
r_scangle_it3.923
r_scbond_it2.235
r_angle_refined_deg1.66
r_mcangle_it1.571
r_mcbond_it0.801
r_nbd_refined0.241
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.144
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3321
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling