3E9K | pdb_00003e9k

Crystal structure of Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HZP	PDB entry 2HZP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	5.12	298	HKynase solution (9 mg/mL in 50 mM HEPES pH 5.1, and 0.1 mM PLP) mixed (1:1 ratio) with a crystallization solution containing 0.05 M MgCl2, 0.1 M Tris-HCl pH 8.0, 25% PEG 3000, 350 mM HHA, pH 5.12, MICROBATCH UNDER OIL, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.444	α = 90
b = 77.124	β = 109.35
c = 94.558	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes	2007-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.007	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	89.09	98.55	0.052			51906	51906			16.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.744	86.66		0.039

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2HZP	1.7	89.09	51906	2802	98.55	0.15512	0.1532	0.15	0.19133	0.19	RANDOM	16.686

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]
-0.44		-0.87	-0.25		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.278
r_dihedral_angle_4_deg	19.569
r_dihedral_angle_3_deg	11.999
r_dihedral_angle_1_deg	5.373
r_scangle_it	4.351
r_scbond_it	2.973
r_mcangle_it	1.65
r_angle_refined_deg	1.065
r_mcbond_it	0.894
r_nbtor_refined	0.306
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.095
r_symmetry_hbond_refined	0.088
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
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 Atoms	Number
Protein Atoms	3547
Nucleic Acid Atoms
Solvent Atoms	632
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing