4UOZ

beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 nucleophile mutant E324A in complex with galactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UNI	PDB ENTRY 4UNI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2 M MGCL2, 0.1 M HEPES PH 7.5, 30% PEG 400 RESERVOIR, 0.1 UL DROP SET UP WITH A 1:1 RATIO OF RESERVOIR TO STOCK SOLUTION CONTAINING 12 MG/ML PROTEIN AND 150 MM 6-GALACTOBIOSE.

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.2	α = 90
b = 167.97	β = 115.64
c = 108.58	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	MARRESEARCH	MIRROR	2013-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3		MAX II	I911-3

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	2.3	30	99.8	0.16	9.64	4.1		95853

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	2.3	2.36	99.8		0.78	2.2	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4UNI	2.3	28.68	91036	4795	99.86	0.18926	0.18613	0.19	0.24813	0.25	RANDOM	23.111

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]
0.37		0.41	-0.24		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.684
r_dihedral_angle_4_deg	20.997
r_dihedral_angle_3_deg	17.904
r_dihedral_angle_1_deg	6.883
r_angle_refined_deg	1.811
r_chiral_restr	0.124
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	16407
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
CCP4	phasing