5K4W

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NADH and L-threonine refined to 1.72 angstroms

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.2M sodium acetate, 0.1M Tris, 30% w/v PEG 4000, NADH (10mM), L-Threonine (30mM)

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.45	α = 90
b = 136.12	β = 90
c = 55.69	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	PIXEL	DECTRIS PILATUS3 6M		2013-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.72	46.32	99.5	0.094	0.997	11	6.4		67909

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	1.72	1.76	100		0.765		6.6

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	1.72	43.14	64406	3443	99.45	0.1545	0.1522	0.1976	RANDOM	27.667

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]
-0.03			-0.08		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.642
r_dihedral_angle_4_deg	17.753
r_dihedral_angle_3_deg	13.554
r_dihedral_angle_1_deg	6.617
r_mcangle_it	3.137
r_mcbond_it	2.339
r_mcbond_other	2.338
r_angle_refined_deg	2.104
r_angle_other_deg	1.094
r_chiral_restr	0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.642
r_dihedral_angle_4_deg	17.753
r_dihedral_angle_3_deg	13.554
r_dihedral_angle_1_deg	6.617
r_mcangle_it	3.137
r_mcbond_it	2.339
r_mcbond_other	2.338
r_angle_refined_deg	2.104
r_angle_other_deg	1.094
r_chiral_restr	0.43
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5012
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	124

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.