4J28

Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4J27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291.15	10.45% PEG 6K, 0.12M ammonium sulfate, 0.095M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.728	α = 90
b = 95.611	β = 91.21
c = 96.988	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	PIXEL	PSI PILATUS 6M		2011-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.73	29.013	98.3	0.045	12.8	3.2	128218	128218

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	1.73	1.82	94.5		0.449	0.449	1.7	3.2	17914

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4J27	1.73	29.01	128119	6409	98.13	0.1717	0.1706	0.1935	RANDOM	34.2843

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]
4.24		-0.86	-0.23		-3.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.448
r_dihedral_angle_4_deg	18.55
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	5.784
r_mcangle_it	3.156
r_mcbond_it	2.434
r_mcbond_other	2.433
r_angle_refined_deg	1.533
r_angle_other_deg	1.047
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.448
r_dihedral_angle_4_deg	18.55
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	5.784
r_mcangle_it	3.156
r_mcbond_it	2.434
r_mcbond_other	2.433
r_angle_refined_deg	1.533
r_angle_other_deg	1.047
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7027
Nucleic Acid Atoms
Solvent Atoms	729
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
REFMAC	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.