3AAW

Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	1.2M Sodium citrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.232	α = 90
b = 162.232	β = 90
c = 133.926	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 4r	mirror	2007-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.978	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	50	99.8	0.056	0.056	27.1	7.6		59981			59.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	100		0.338	5.8	7.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2HMF and 2DTJ	2.5	43.56	59980	56782	3022	99.71	0.21188	0.21188	0.20985	0.25029	RANDOM	45.963

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]
-1.36			-1.36		2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.572
r_dihedral_angle_4_deg	17.084
r_dihedral_angle_3_deg	15.716
r_dihedral_angle_1_deg	5.429
r_scangle_it	2.122
r_scbond_it	1.2
r_angle_refined_deg	1.066
r_mcangle_it	0.94
r_angle_other_deg	0.838
r_mcbond_it	0.493

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.572
r_dihedral_angle_4_deg	17.084
r_dihedral_angle_3_deg	15.716
r_dihedral_angle_1_deg	5.429
r_scangle_it	2.122
r_scbond_it	1.2
r_angle_refined_deg	1.066
r_mcangle_it	0.94
r_angle_other_deg	0.838
r_mcbond_it	0.493
r_chiral_restr	0.063
r_mcbond_other	0.058
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	8199
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	62

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.