5K4Q

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ refined to 2.3 angstroms

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.2M lithium sulphate, 0.1M Tris, 30% w/v PEG 4K, pH 8.5, NAD+ (0.09mM)

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.63	α = 90
b = 277.72	β = 90
c = 56	γ = 90

Symmetry
Space Group	P 21 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		2011-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9334	ESRF	ID14-4

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	2.3	48.143	99.2	0.12	11.2	6.7		93173

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	2.3	2.42	95.3		0.276	2.7	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.3	48.143	88435	4653	99.17	0.1775	0.174	0.2438	RANDOM	21.09

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			0.05		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_dihedral_angle_4_deg	18.153
r_dihedral_angle_3_deg	16.369
r_dihedral_angle_1_deg	6.958
r_mcangle_it	2.554
r_angle_refined_deg	1.713
r_mcbond_it	1.592
r_mcbond_other	1.59
r_angle_other_deg	0.874
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_dihedral_angle_4_deg	18.153
r_dihedral_angle_3_deg	16.369
r_dihedral_angle_1_deg	6.958
r_mcangle_it	2.554
r_angle_refined_deg	1.713
r_mcbond_it	1.592
r_mcbond_other	1.59
r_angle_other_deg	0.874
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14974
Nucleic Acid Atoms
Solvent Atoms	928
Heterogen Atoms	325

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.