3E0F

Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	0.0200M CaCl2, 30.0000% MPD, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.46	α = 90
b = 102.46	β = 90
c = 54.17	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.4	29.579	99.7	0.119				12857		-3	36.482

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	2.4	2.49	99.3		0.525	2.7

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	SAD	THROUGHOUT	2.4	29.579	12839	626	99.89	0.152	0.149	0.207	RANDOM	24.211

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]
0.95	0.48		0.95		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.641
r_dihedral_angle_4_deg	20.646
r_dihedral_angle_3_deg	15.435
r_scangle_it	7.63
r_dihedral_angle_1_deg	5.906
r_scbond_it	5.557
r_mcangle_it	3.087
r_mcbond_it	2.122
r_angle_refined_deg	1.47
r_angle_other_deg	0.943
r_mcbond_other	0.436
r_nbd_refined	0.2
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.181
r_symmetry_vdw_other	0.18
r_symmetry_vdw_refined	0.172
r_nbtor_refined	0.17
r_symmetry_hbond_refined	0.128
r_nbtor_other	0.088
r_chiral_restr	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing