2GN1

Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 2.2A resolution (Triclinic form with one dimer of TdcB in the asymmetric unit)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.1 M citrate buffer pH 6.0, 20% PEG 3350 and 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.317	α = 103.09
b = 55.3	β = 94.7
c = 67.235	γ = 112.94

Symmetry
Space Group	P 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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic mirror	2005-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.542

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	2.2	30	94.7	0.053	22.18	12.19		29556			31.42

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	2.2	2.28	84.5		0.222	4.98		2494

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0)	2.2	25	26557	26557	1405	94.32	0.21183	0.20964	0.25291	RANDOM	32.816

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]
1.76	2.34	0.94	2.5	0.92	-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.666
r_dihedral_angle_3_deg	12.703
r_dihedral_angle_4_deg	12.482
r_dihedral_angle_1_deg	5.47
r_scangle_it	1.538
r_angle_refined_deg	1.025
r_scbond_it	0.885
r_angle_other_deg	0.741
r_mcangle_it	0.563
r_mcbond_it	0.312
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.175
r_symmetry_vdw_other	0.168
r_nbtor_refined	0.163
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.145
r_symmetry_metal_ion_refined	0.104
r_symmetry_hbond_refined	0.088
r_nbtor_other	0.079
r_mcbond_other	0.057
r_chiral_restr	0.056
r_metal_ion_refined	0.043
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4789
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing