5K50 | pdb_00005k50

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ and L-allo-threonine refined to 2.23 angstroms

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.1M tri-sodium citrate, 30% w/v PEG 4K, 0.2M ammonium acetate, NAD+ (10mM), L-allo-threonine (30mM)

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.03	α = 90
b = 273.06	β = 90
c = 55.8	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 PILATUS 2M		2013-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

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	2.26	31.09	90.4	0.151	0.862	5.6	1.9		154520

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	2.26	2.34	92.5		0.403		1.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.26	31.09	91289	4815	99.65	0.211	0.2073	0.21	0.2808	0.28	RANDOM	33.758

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]
-0.02			0.03		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.375
r_dihedral_angle_4_deg	17.896
r_dihedral_angle_3_deg	16.765
r_dihedral_angle_1_deg	7.507
r_mcangle_it	3.387
r_mcbond_it	2.186
r_mcbond_other	2.186
r_angle_refined_deg	1.649
r_angle_other_deg	0.862
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.375
r_dihedral_angle_4_deg	17.896
r_dihedral_angle_3_deg	16.765
r_dihedral_angle_1_deg	7.507
r_mcangle_it	3.387
r_mcbond_it	2.186
r_mcbond_other	2.186
r_angle_refined_deg	1.649
r_angle_other_deg	0.862
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14958
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	344

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
PHASER	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.