Experiment: 3N9B

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG 5000 monomethylether (MME) (20 - 30%), 100 mM 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.8 - 7.0, 200 mM ammonium sulfate, and 10 mM yttrium (III) chloride at 22 C. , VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.583	α = 102.32
b = 45.55	β = 109.43
c = 53.384	γ = 104.59

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	130	CCD	ADSC QUANTUM 315	See NSLS X25 Beamline Description	2010-02-20	M	SINGLE WAVELENGTH
2	1		CCD	ADSC QUANTUM 210	See NSLS X12C Beamline Description	2010-02-20
3	1		IMAGE PLATE	RIGAKU RAXIS IV++	Osmic confocal mirrors	2010-02-10

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.19, 0.99, 0.73	NSLS	X12C
2	SYNCHROTRON	NSLS BEAMLINE X25	1.19, 0.99, 0.73	NSLS	X25
3	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.92	50	95.6	0.087	25.9	7.4	25728	24596		-3	26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.92	1.95	93		4.8	2.1	1272

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	1.92	37.395	0.06	23992	2387	92.95	0.1527	0.1475	0.1443	0.1988	0.1969	10% selected at random in CCP4/Unique

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]
5.3212	-1.2709	-1.1842	-1.6351	0.4754	-3.7302

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.969
f_angle_d	1.249
f_chiral_restr	0.1
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2439
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	34

Software

Software
Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling