8IBS

Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E160A/E318A mutant in complex with galactose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	0.1 M MES-NaOH buffer (pH 6.5), 0.1 M (CH3COO)2Mg, 10% PEG 10000, 25% glycerol, 30 mM lacto-N-tetraose (cleaved)

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.47	α = 90
b = 182.691	β = 125.73
c = 143.263	γ = 90

Symmetry
Space Group	C 1 2 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		2012-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	48.57	98.3	0.097	0.058	0.997	9.5	3.7		376638			22.06

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	83		0.935	0.672	0.545	1.1	2.8

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	1.9	48.61	357918	18712	98.26	0.18935	0.18731	0.22841	RANDOM	24.001

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]
-0.54		-0.36	2.4		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.393
r_dihedral_angle_2_deg	7.642
r_dihedral_angle_1_deg	6.928
r_long_range_B_refined	4.745
r_long_range_B_other	4.672
r_scangle_other	3.763
r_mcangle_it	2.752
r_mcangle_other	2.752
r_scbond_it	2.453
r_scbond_other	2.453
r_mcbond_it	1.931
r_mcbond_other	1.931
r_angle_refined_deg	1.405
r_angle_other_deg	0.496
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32856
Nucleic Acid Atoms
Solvent Atoms	2870
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing