4L50

Crystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different analogs reveal distinct mechanisms for ligand recognition

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	5% PEG3350, 0.1 M Bis-Tris, 0.1 M NaCl, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.809	α = 90
b = 116.809	β = 90
c = 79.975	γ = 120

Symmetry
Space Group	P 65

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	ADSC QUANTUM 315r		2012-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.10000	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	34.52	97.3			35349	33513	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	92.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.1	34.52	33513	1782	97.1	0.16902	0.16644	0.21806	RANDOM	35.457

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]
-0.04	-0.04		-0.04		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.51
r_dihedral_angle_4_deg	20.334
r_dihedral_angle_3_deg	16.045
r_dihedral_angle_1_deg	6.57
r_angle_refined_deg	1.983
r_angle_other_deg	0.949
r_chiral_restr	0.27
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.51
r_dihedral_angle_4_deg	20.334
r_dihedral_angle_3_deg	16.045
r_dihedral_angle_1_deg	6.57
r_angle_refined_deg	1.983
r_angle_other_deg	0.949
r_chiral_restr	0.27
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3625
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	34

Software

Software
Software Name	Purpose
ADSC	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

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.