2Y2W

Elucidation of the substrate specificity and protein structure of AbfB, a family 51 alpha-L-arabinofuranosidase from Bifidobacterium longum.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PZ3	PDB ENTRY 1PZ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION			ABFB CRYSTALS WERE OBTAINED BY MIXING 1 MICROLITER CONCENTRATED PROTEIN SOLUTION WITH 3 MICROLITER CRYSTALLIZATION SOLUTION CONTAINING 0.2 M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 20% W/V POLYETHYLENE GLYCOL 3350, USING THE VAPOR-DIFFUSION METHOD WITH HANGING OR SITTING DROPS AT 20-24 C.

Crystal Properties
Matthews coefficient	Solvent content
2.44	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.469	α = 90
b = 165.811	β = 90
c = 184.297	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r		2009-04-25	M	SINGLE WAVELENGTH

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

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	2.5	20	99.8	0.12	8.9	4.1		109183		2.4

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	2.5	2.64	100		0.56	2.4	4.1

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	PDB ENTRY 1PZ3	2.5	20	109183	5776	99.82	0.22263	0.22014	0.26986	RANDOM	37.259

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]
-0.71			-2.59		3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.517
r_dihedral_angle_3_deg	15.029
r_dihedral_angle_4_deg	14.891
r_dihedral_angle_1_deg	4.965
r_angle_refined_deg	0.92
r_scangle_it	0.694
r_mcangle_it	0.439
r_scbond_it	0.396
r_mcbond_it	0.236
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23544
Nucleic Acid Atoms
Solvent Atoms	699
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing