2ZYJ

Crystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-glutamate), from Thermus thermophilus HB27

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CBF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	16% PEG 3350, 0.1M HEPES, 0.2M Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.761	α = 90
b = 93.346	β = 90
c = 150.827	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	95	CCD	ADSC QUANTUM 210	mirrors	2009-01-21	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	1.67	50	99.2	0.097	0.097				91922	2.2	2.2

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	1.67	1.73	99.8		0.588			9045

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3CBF	1.67	30.47	86525	4563	98.96	0.19604	0.19337	0.24611	RANDOM	16.178

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					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.488
r_dihedral_angle_4_deg	19.936
r_dihedral_angle_3_deg	15.844
r_dihedral_angle_1_deg	5.568
r_scangle_it	3.3
r_scbond_it	2.091
r_angle_refined_deg	1.515
r_mcangle_it	1.245
r_mcbond_it	0.81
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.488
r_dihedral_angle_4_deg	19.936
r_dihedral_angle_3_deg	15.844
r_dihedral_angle_1_deg	5.568
r_scangle_it	3.3
r_scbond_it	2.091
r_angle_refined_deg	1.515
r_mcangle_it	1.245
r_mcbond_it	0.81
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.225
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6188
Nucleic Acid Atoms
Solvent Atoms	956
Heterogen Atoms	50

Software

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