3O0F

Crystal structure of a putative metal-dependent phosphoesterase (BAD_1165) from bifidobacterium adolescentis atcc 15703 at 1.94 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.71	277	24.0000% 2-methyl-2,4-pentanediol, 0.0200M calcium acetate, 0.1M sodium acetate pH 4.71, 0.005 M adenosine 5'-monophosphate, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.341	α = 90
b = 103.341	β = 90
c = 54.744	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 315		2010-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

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	1.94	44.748	99.6	0.167	12.54			24784		-3	18.988

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	1.94	2.01	97.7		0.799	2.6

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	1.94	44.748	24761	1241	99.62	0.1613	0.1597	0.1916	RANDOM	23.7813

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]
0.41	0.2		0.41		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.8
r_dihedral_angle_4_deg	20.717
r_dihedral_angle_3_deg	14.018
r_scangle_it	7.989
r_dihedral_angle_1_deg	6.107
r_scbond_it	5.726
r_mcangle_it	3.245
r_mcbond_it	1.973
r_angle_refined_deg	1.607
r_angle_other_deg	1.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.8
r_dihedral_angle_4_deg	20.717
r_dihedral_angle_3_deg	14.018
r_scangle_it	7.989
r_dihedral_angle_1_deg	6.107
r_scbond_it	5.726
r_mcangle_it	3.245
r_mcbond_it	1.973
r_angle_refined_deg	1.607
r_angle_other_deg	1.176
r_mcbond_other	0.593
r_chiral_restr	0.132
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2151
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	39

Software

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

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 R01GM133198.