2R2D

Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	298	35% glycerol anhydrous and 0.26 M ammonium dihydrogen phosphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.146	α = 90
b = 158.033	β = 104.48
c = 80.439	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.97946	SSRL	BL9-1

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	1.75	79.06	96.8	0.062	16.6	2.9		185201			40.4

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	1.75	1.81	79.1		0.606	1.1	2.1	15044

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	SAD	THROUGHOUT	1.75	18.1	1	175810	9324	96.52	0.16169	0.15898	0.21267	RANDOM	35.798

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]
0.24		0.19	0.83		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.807
r_dihedral_angle_4_deg	18.107
r_dihedral_angle_3_deg	15.795
r_dihedral_angle_1_deg	5.967
r_scangle_it	4.604
r_scbond_it	3.203
r_mcangle_it	1.972
r_angle_refined_deg	1.526
r_mcbond_it	1.279
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.807
r_dihedral_angle_4_deg	18.107
r_dihedral_angle_3_deg	15.795
r_dihedral_angle_1_deg	5.967
r_scangle_it	4.604
r_scbond_it	3.203
r_mcangle_it	1.972
r_angle_refined_deg	1.526
r_mcbond_it	1.279
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.217
r_symmetry_hbond_refined	0.21
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.126
r_metal_ion_refined	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12924
Nucleic Acid Atoms
Solvent Atoms	1521
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

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.