3R76

Crystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC) synthase PhzE from Burkholderia lata 383 in complex with benzoate, pyruvate and glutamine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R75	PDB ENTRY 3R75

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	276	0.1 M HEPES, 0.2 M Mg-chloride, 22% isopropanol, pre-incubation on ice for 30' with 50 mM Mg-chloride, 20 mM glutamine, 20 mM chorismate, streak-seeding, pH 7.1, vapor diffusion, hanging drop, temperature 276K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 258.166	α = 90
b = 97.792	β = 90
c = 53.988	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	MARMOSAIC 225 mm CCD	SI(111)	2009-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.979	SLS	X10SA

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	2.6	29.664	99.8	0.06	17.71			43071		-3	47.384

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	2.6	2.7	100		0.357	4.45

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3R75	2.6	29.66	43043	2227	99.84	0.1665	0.1633	0.225	RANDOM	52.2518

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]
-1.57			-1.42		2.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.861
r_dihedral_angle_4_deg	18.717
r_dihedral_angle_3_deg	16.607
r_dihedral_angle_1_deg	6.301
r_angle_other_deg	2.461
r_angle_refined_deg	1.572
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_bond_other_d	0.007
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.861
r_dihedral_angle_4_deg	18.717
r_dihedral_angle_3_deg	16.607
r_dihedral_angle_1_deg	6.301
r_angle_other_deg	2.461
r_angle_refined_deg	1.572
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9278
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.