3S30

Crystal structure of a putative glycoside hydrolase (BVU_0247) from Bacteroides vulgatus ATCC 8482 at 2.46 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	277	20.0% polyethylene glycol 3350, 0.2M ammonium nitrate, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.745	α = 90
b = 146.745	β = 90
c = 91.51	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); single crystal Si(111) bent monochromator (ho rizontal focusing)	2009-07-07	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)	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	2.46	29.656	99.1	0.094	0.094	12.1	4.2		40478

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.46	2.52	98.7		0.811	0.811	0.9	4.2	2977

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	2.46	29.656	40475	2033	99.21	0.2334	0.2325	0.2506	RANDOM	63.9867

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]
0.46	0.23		0.46		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.569
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_4_deg	8.535
r_dihedral_angle_1_deg	6.274
r_scangle_it	4.659
r_scbond_it	3.563
r_mcangle_it	1.812
r_angle_refined_deg	1.134
r_mcbond_it	1.003
r_angle_other_deg	0.799

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.569
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_4_deg	8.535
r_dihedral_angle_1_deg	6.274
r_scangle_it	4.659
r_scbond_it	3.563
r_mcangle_it	1.812
r_angle_refined_deg	1.134
r_mcbond_it	1.003
r_angle_other_deg	0.799
r_mcbond_other	0.27
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3972
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	2

Software

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

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 R01GM157729.