Experiment: 3S1T

Structure of the regulatory domain of aspartokinase (Rv3709c; AK-beta) in complex with threonine from Mycobacterium tuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	ammonium sulphate, bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.7	α = 90
b = 63.43	β = 90
c = 108.85	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2010-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	1.000	EMBL/DESY, HAMBURG	X12

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.63	99	99			48122	47641	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.65	100

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 (All)	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	2DTJ	1.63	30	47148	45214	1450	98.95	0.19318	0.19318	0.19258	0.1926	0.21143	0.2099	RANDOM	23.877

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]
0.34			-0.2		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.356
r_dihedral_angle_4_deg	18.015
r_dihedral_angle_3_deg	14.689
r_dihedral_angle_1_deg	5.931
r_angle_refined_deg	1.778
r_chiral_restr	0.118
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2409
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement