4N0R

Crystal structure of a putative glycoside hydrolase (BVU_0362) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.67	293	0.01M nickel (II) chloride, 22.0% polyethylene glycol monomethyl ether 2000, 0.2M NDSB-256, 0.1M TRIS pH 8.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.439	α = 90
b = 67.684	β = 90
c = 90.066	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2013-08-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.9792, 0.97868	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	1.8	29.211	95.4	0.075	7.89	3.74		127394		-3	21.082

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	1.8	1.86	89.8		0.563	1.5

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	1.8	29.211	127320	6400	98.67	0.1516	0.1501	0.1796	RANDOM	26.3603

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]
-1.19			1.57		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.28
r_dihedral_angle_4_deg	15.522
r_dihedral_angle_3_deg	11.19
r_dihedral_angle_1_deg	6.675
r_mcangle_it	3.392
r_mcbond_it	2.577
r_mcbond_other	2.568
r_angle_refined_deg	1.6
r_angle_other_deg	1.121
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.28
r_dihedral_angle_4_deg	15.522
r_dihedral_angle_3_deg	11.19
r_dihedral_angle_1_deg	6.675
r_mcangle_it	3.392
r_mcbond_it	2.577
r_mcbond_other	2.568
r_angle_refined_deg	1.6
r_angle_other_deg	1.121
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8344
Nucleic Acid Atoms
Solvent Atoms	1264
Heterogen Atoms	60

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.