4F4E

Crystal structure of Aromatic-amino-acid aminotransferase from Burkholderia pseudomallei covalently bound to pyridoxal phosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Emerald Bio JCSG+ screen C1: 20% PEG8000, 100 mM phosphate/citrate, pH 4.2, 200 mM sodium chloride, 36.1 mg/mL BupsE.01471.a.A1 PW 34948 + 2.5 mM PLP, tray 233390c1, cryoprotectant: 10/20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.92	α = 90
b = 74.82	β = 90
c = 85.28	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	CCD	RIGAKU SATURN 944+		2012-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	50	99.7	0.06	20.33	5	80697	80481		-3	22.744

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	1.8	1.85	98.7		0.465	2.47	3

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 ENTRY 4EFF	1.8	50	80697	80427	4037	99.73	0.1625	0.1625	0.1607	0.1964	RANDOM	17.3325

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]
-0.07			0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.77
r_dihedral_angle_4_deg	18.986
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	5.605
r_angle_refined_deg	1.586
r_angle_other_deg	0.963
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.77
r_dihedral_angle_4_deg	18.986
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	5.605
r_angle_refined_deg	1.586
r_angle_other_deg	0.963
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5996
Nucleic Acid Atoms
Solvent Atoms	859
Heterogen Atoms	16

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.