4ZRX

Crystal structure of a putative alpha-L-fucosidase (BACOVA_04357) from Bacteroides ovatus ATCC 8483 at 1.59 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	24.0% polyethylene glycol 3350, 0.11M potassium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.021	α = 90
b = 71.754	β = 106.98
c = 73.106	γ = 90

Symmetry
Space Group	P 1 21 1

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	Vertical focusing mirror; double crystal Si(111) monochromator	2014-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	.979230	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.59	28.599	97.5	0.043	0.052	14.68	3.2		81860		-3	21.531

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.59	1.65	96.4		0.576	0.691	2

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	1.59	28.599	81838	4082	97.65	0.1526	0.1515	0.1752	RANDOM	28.6366

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]
-0.27		-0.51	-2.14		2.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.068
r_dihedral_angle_4_deg	16.526
r_dihedral_angle_3_deg	12.987
r_dihedral_angle_1_deg	6.24
r_angle_refined_deg	1.648
r_mcangle_it	1.593
r_mcbond_it	1.021
r_mcbond_other	1.02
r_angle_other_deg	0.943
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.068
r_dihedral_angle_4_deg	16.526
r_dihedral_angle_3_deg	12.987
r_dihedral_angle_1_deg	6.24
r_angle_refined_deg	1.648
r_mcangle_it	1.593
r_mcbond_it	1.021
r_mcbond_other	1.02
r_angle_other_deg	0.943
r_chiral_restr	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4667
Nucleic Acid Atoms
Solvent Atoms	595
Heterogen Atoms	28

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
SHELXD	phasing
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.