6YXZ | pdb_00006yxz

Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		generated by MrBUMP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	21.6 mg/mL of purified protein in the buffer of tris 25 mM pH 8.0 and NaCl 200 mM is mixed with PEG 3350 23%, 0.1 M bis-tris propane PH 6.5 and 0.2 M NaBr at 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.566	α = 90
b = 126.75	β = 90
c = 152.71	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 EIGER2 XE 16M		2019-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.75	63.38	100	0.997	9	7.4		111519

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	1.75	1.78	100		1.654	0.969	0.61	1.1	7.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	generated by MrBUMP	1.75	63.38	111416	5615	99.947	0.163	0.1601	0.17	0.2197	0.22	27.359

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]
-3.781			1.429		2.352

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.127
r_dihedral_angle_4_deg	15.553
r_dihedral_angle_3_deg	12.33
r_dihedral_angle_1_deg	7.043
r_lrange_it	6.574
r_lrange_other	6.329
r_scangle_it	5.819
r_scangle_other	5.818
r_mcangle_it	5.197
r_mcangle_other	5.197
r_scbond_other	4.798
r_scbond_it	4.797
r_mcbond_it	4.325
r_mcbond_other	4.323
r_rigid_bond_restr	3.102
r_angle_refined_deg	1.511
r_angle_other_deg	1.41
r_nbd_other	0.212
r_nbd_refined	0.204
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.072
r_metal_ion_refined	0.023
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5290
Nucleic Acid Atoms
Solvent Atoms	641
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
SHELXDE	phasing