3WX9

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, GLA, 4AD, 2OG, GLU and KYA


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 PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.769α = 90
b = 70.997β = 90.02
c = 136.704γ = 90
Symmetry
Space GroupC 1 2 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 BL38B11.0SPring-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
11.585096.80.0493.5109166
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)
11.581.6499.30.5452.073.4

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 3AOV1.5850103708545896.610.182880.180460.22975RANDOM25.781
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]
-1.58-0.181.510.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.241
r_dihedral_angle_4_deg21.744
r_dihedral_angle_3_deg15.127
r_dihedral_angle_1_deg8.734
r_scangle_it6.02
r_scbond_it3.844
r_angle_refined_deg2.503
r_mcangle_it2.439
r_mcbond_it1.461
r_chiral_restr0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.241
r_dihedral_angle_4_deg21.744
r_dihedral_angle_3_deg15.127
r_dihedral_angle_1_deg8.734
r_scangle_it6.02
r_scbond_it3.844
r_angle_refined_deg2.503
r_mcangle_it2.439
r_mcbond_it1.461
r_chiral_restr0.174
r_bond_refined_d0.03
r_gen_planes_refined0.014
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_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 Atoms6494
Nucleic Acid Atoms
Solvent Atoms829
Heterogen Atoms124

Software

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