4J27

Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in a novel crystal form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291.15	17% PEG 6K, 0.124M ammonium sulfate, 0.1M imidazole 2 parts protein: 3 mother liquor, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.15	α = 90
b = 96.55	β = 91.3
c = 97.27	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	MAR CCD 165 mm		2011-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	1.59	30.666	100	0.112	8.2	3.8	164706	164706

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	1.59	1.68	99.9		0.878	0.878	0.9	3.7	23967

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	2WVV	1.59	30.666	159881	8454	99.94	0.1587	0.1577	0.1775	RANDOM	15.8145

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]
1.12		-0.29	0.03		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.036
r_dihedral_angle_4_deg	20.764
r_dihedral_angle_3_deg	11.888
r_dihedral_angle_1_deg	5.805
r_mcangle_it	1.719
r_angle_refined_deg	1.477
r_mcbond_it	1.101
r_mcbond_other	1.1
r_angle_other_deg	1.056
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.036
r_dihedral_angle_4_deg	20.764
r_dihedral_angle_3_deg	11.888
r_dihedral_angle_1_deg	5.805
r_mcangle_it	1.719
r_angle_refined_deg	1.477
r_mcbond_it	1.101
r_mcbond_other	1.1
r_angle_other_deg	1.056
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7075
Nucleic Acid Atoms
Solvent Atoms	1059
Heterogen Atoms	69

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	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 R01GM157729.