5WZR

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.02M MgCl2, 0.1M HEPES-NaOH, 7.5% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.628	α = 90
b = 128.478	β = 90
c = 176.885	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 PILATUS 2M-F		2016-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.1000	Photon Factory	BL-1A

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	2.79	103.95	99.7	0.057	19.6	6.3		37110

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.85	100		0.518	0.979	2.4	6.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.79	103.95	35202	1852	98.66	0.23315	0.22899	0.31325	RANDOM	79.962

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]
0.01			0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.383
r_dihedral_angle_4_deg	18.17
r_dihedral_angle_3_deg	16.76
r_long_range_B_other	10.608
r_long_range_B_refined	10.607
r_dihedral_angle_1_deg	8.013
r_mcangle_it	7.72
r_mcangle_other	7.72
r_scangle_other	6.606
r_mcbond_it	4.863
r_mcbond_other	4.855
r_scbond_it	4.027
r_scbond_other	4.027
r_angle_refined_deg	1.461
r_angle_other_deg	0.858
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
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	9972
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing