Experiment: 3IAU

The structure of the processed form of threonine deaminase isoform 2 from Solanum lycopersicum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	277	Protein Solution (10 mg/ml protein, 0.05 M NaCl, 0.003 M NaN3, 0.005 M Bis-Tris pH 7) mixed in a 1:1 ratio with the Well Solution (32% Polyethylene glycol 1500, 0.1 M LiSO4, 0.1 M Sodium Acetate pH 4.5). Cryoprotected with 32% Polyethylene glycol 1500, 0.1 M LiSO4, 5% ethylene glycol, 0.1 M Sodium Acetate pH 4.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.42	72.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.834	α = 90
b = 136.834	β = 90
c = 254.226	γ = 120

Symmetry
Space Group	P 61 2 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	MARMOSAIC 300 mm CCD	mirrors and beryllium lenses	2009-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97957	APS	23-ID-D

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	2.35	50	100	0.133	7.5	21.5		58877			26.65

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)
	2.35	2.43	100		0.676		19.9	5776

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.353	48.559	1.34	58785	2979	99.8	0.166	0.164	0.162	0.199	0.1968	32.753

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]
1.684			1.684		-3.368

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.409
f_angle_d	0.914
f_chiral_restr	0.061
f_bond_d	0.005
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5324
Nucleic Acid Atoms
Solvent Atoms	654
Heterogen Atoms	40

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction