8P1S

Bifidobacterium asteroides alpha-L-fucosidase (TT1819) in complex with fucose.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.12M Diethylene glycol; 0.12M Triethylene glycol; 0.12M Tetraethylene glycol; 0.12M Pentaethylene glycol, 0.1M Tris (base); BICINE pH 8.5, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.058	α = 90
b = 142.765	β = 90
c = 167.202	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	PIXEL	DECTRIS PILATUS3 X 6M		2017-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97625	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.9	108.56	100	0.246	0.262	0.086	0.998	9.2	17.5		167861

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93			9.946	10.726	3.866	0.215		14.9

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	83.741	167720	8366	99.95	0.171	0.1689	0.2069	38.507

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]
-1.975			1.839		0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.697
r_dihedral_angle_3_deg	15.236
r_dihedral_angle_2_deg	14.914
r_lrange_it	7.313
r_lrange_other	7.309
r_dihedral_angle_1_deg	6.668
r_scangle_it	6.302
r_scangle_other	6.302
r_scbond_it	4.595
r_scbond_other	4.595
r_mcangle_it	4.192
r_mcangle_other	4.192
r_mcbond_it	3.282
r_mcbond_other	3.273
r_angle_refined_deg	1.924
r_angle_other_deg	0.646
r_nbd_other	0.308
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.228
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_5	0.074
r_ncsr_local_group_9	0.07
r_ncsr_local_group_3	0.067
r_ncsr_local_group_4	0.067
r_ncsr_local_group_1	0.066
r_ncsr_local_group_7	0.066
r_ncsr_local_group_6	0.065
r_ncsr_local_group_2	0.063
r_symmetry_xyhbond_nbd_other	0.061
r_ncsr_local_group_8	0.06
r_ncsr_local_group_10	0.06
r_ncsr_local_group_12	0.058
r_ncsr_local_group_15	0.058
r_ncsr_local_group_14	0.057
r_ncsr_local_group_13	0.055
r_ncsr_local_group_11	0.053
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16170
Nucleic Acid Atoms
Solvent Atoms	733
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing