3E2Z | pdb_00003e2z

Crystal structure of mouse kynurenine aminotransferase III in complex with kynurenine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	21% PEG 400, 150 mM CaCl2, 10% Glycerol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.49	α = 90
b = 91.49	β = 90
c = 233.501	γ = 90

Symmetry
Space Group	P 43 21 2

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		2008-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8	30	95.6	0.12		11.9	25229	24119

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9			0.39		3.7

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 2ZJG	2.81	29.64	22779	1227	95.59	0.19394	0.19172	0.19	0.23654	0.24	RANDOM	22.643

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.919
r_dihedral_angle_3_deg	22.06
r_dihedral_angle_4_deg	18.992
r_dihedral_angle_1_deg	9.897
r_scangle_it	4.514
r_scbond_it	2.97
r_angle_refined_deg	2.205
r_mcangle_it	1.903
r_mcbond_it	1.036
r_chiral_restr	0.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.919
r_dihedral_angle_3_deg	22.06
r_dihedral_angle_4_deg	18.992
r_dihedral_angle_1_deg	9.897
r_scangle_it	4.514
r_scbond_it	2.97
r_angle_refined_deg	2.205
r_mcangle_it	1.903
r_mcbond_it	1.036
r_chiral_restr	0.357
r_nbtor_refined	0.339
r_nbd_refined	0.279
r_symmetry_vdw_refined	0.238
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.176
r_bond_refined_d	0.024
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6521
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.