2EAC

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	0.1M Tris (pH7.0), 10% iso-propanol, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.668	α = 90
b = 111.702	β = 95.31
c = 98.346	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	ADSC QUANTUM 315		2005-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	2.1	98.06	100	0.112		7.2	113829	113799

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	99.8		0.337		6.6	11323

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	48.97	108104	5697	99.92	0.15264	0.15024	0.19757	RANDOM	17.022

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]
0.16		-1.12	-0.98		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.552
r_dihedral_angle_4_deg	20.015
r_dihedral_angle_3_deg	13.624
r_dihedral_angle_1_deg	6.326
r_scangle_it	3.392
r_scbond_it	2.296
r_angle_refined_deg	1.505
r_mcangle_it	1.31
r_mcbond_it	0.827
r_nbtor_refined	0.303
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.174
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.102
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13462
Nucleic Acid Atoms
Solvent Atoms	1685
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing