8QF8

GH146 beta-L-arabinofuranosidase from Bacteroides thetaioatomicron in complex with beta-l-arabinofurano cyclophellitol aziridine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	15-17% PEG 3350, MES pH 6.25-6.5, 0.2M ammonium formate, seeding from similar conditions

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.84	α = 90
b = 98.549	β = 90
c = 196.584	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 EIGER X 16M		2023-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

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	2.4	55.9	100	0.101	0.109	0.041	0.994	16.8	13.7		72064

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	2.4	2.45			1.138	1.237	0.481	0.83		12.7

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	THROUGHOUT	2.4	55.899	71982	3622	99.963	0.191	0.1896	0.2208	61.794

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]
3.914			-1.045		-2.868

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.086
r_dihedral_angle_3_deg	13.437
r_dihedral_angle_1_deg	7.085
r_dihedral_angle_2_deg	6.964
r_lrange_it	6.057
r_lrange_other	6.052
r_scangle_it	3.742
r_scangle_other	3.741
r_mcangle_it	3.134
r_mcangle_other	3.134
r_scbond_it	2.31
r_scbond_other	2.309
r_mcbond_it	2.016
r_mcbond_other	2.016
r_angle_refined_deg	1.259
r_angle_other_deg	0.492
r_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.163
r_symmetry_nbd_other	0.153
r_symmetry_nbd_refined	0.148
r_nbd_other	0.144
r_metal_ion_refined	0.134
r_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.067
r_ncsr_local_group_1	0.064
r_chiral_restr	0.062
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12421
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
DIALS	data collection
Aimless	data scaling
MOLREP	phasing
DIALS	data reduction