3HFT

Crystal structure of a putative polysaccharide deacetylase involved in o-antigen biosynthesis (wbms, bb0128) from bordetella bronchiseptica at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	20.0000% MPD, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.724	α = 90
b = 74.724	β = 90
c = 142.692	γ = 90

Symmetry
Space Group	P 41 21 2

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 collimating mirror, toroid focusing mirror	2008-12-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97985,0.97968	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.9	29.566	100	0.085	0.085	0.091	15.5	7.2		32707			29.568

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	100		0.902	0.902	0.971	2.1	7.3	2365

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	MAD	THROUGHOUT	1.9	29.566	32639	1654	99.98	0.163	0.162	0.184	RANDOM	38.386

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]
0.6			0.6		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.329
r_dihedral_angle_4_deg	14.965
r_dihedral_angle_3_deg	12.131
r_scangle_it	5.929
r_dihedral_angle_1_deg	4.564
r_scbond_it	4.458
r_mcangle_it	2.584
r_mcbond_it	1.791
r_angle_refined_deg	1.437
r_angle_other_deg	0.918
r_mcbond_other	0.455
r_symmetry_vdw_other	0.296
r_symmetry_vdw_refined	0.266
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.215
r_nbd_other	0.213
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.092
r_nbtor_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1971
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	33

Software

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