2EAB

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	0.1M TRIS (PH 7.5), 10% ISOPROPANOL, 10% PEG6000, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.183	α = 90
b = 112.035	β = 94.74
c = 98.317	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	90	CCD	ADSC QUANTUM 210		2005-06-29	M	SINGLE WAVELENGTH
2	1	x-ray	90	CCD	ADSC QUANTUM 210		2005-06-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9792, 0.97936, 0.91837	SSRL	BL9-2

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
1,2	1.12	50	91.1	0.055	30			643080

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)
	1.12	1.16	77.6		0.369	2.5

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	1.12	35.05	643080	33894	91.6	0.176	0.175	0.189	RANDOM	14.05

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]
0.02		-0.01	-0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.271
r_dihedral_angle_4_deg	14.593
r_dihedral_angle_3_deg	11.133
r_dihedral_angle_1_deg	5.842
r_scangle_it	1.791
r_scbond_it	1.238
r_angle_refined_deg	1.168
r_mcangle_it	0.734
r_mcbond_it	0.442
r_nbtor_refined	0.301
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.13
r_chiral_restr	0.075
r_symmetry_hbond_refined	0.074
r_xyhbond_nbd_refined	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
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_refined
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	13475
Nucleic Acid Atoms
Solvent Atoms	3383
Heterogen Atoms	82

Software

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