6Z14 | pdb_00006z14

Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhexosaminidase E553Q variant in complex with 4MU-6SGlcNAc-derived oxazoline

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YXZ

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 21%, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 0.2 M NANO3 AT 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.423	α = 90
b = 124.884	β = 90
c = 151.682	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		2020-03-02	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)	R Merge I (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	1.67	64.82	100	0.116	0.996	7.4	7		120710

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	1.67	1.7			0.732	0.755	1	6.9

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	6YXZ	1.67	64.82	120604	6030	99.938	0.163	0.1604	0.17	0.2055	0.21	26.849

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]
1.842			-0.959		-0.883

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.727
r_dihedral_angle_4_deg	16.402
r_dihedral_angle_3_deg	13.251
r_dihedral_angle_1_deg	7.166
r_lrange_it	4.983
r_lrange_other	4.734
r_scangle_it	4.531
r_scangle_other	4.53
r_mcangle_it	3.675
r_mcangle_other	3.675
r_scbond_it	3.643
r_scbond_other	3.643
r_mcbond_it	2.956
r_mcbond_other	2.954
r_rigid_bond_restr	2.059
r_angle_refined_deg	1.44
r_angle_other_deg	1.39
r_nbd_other	0.226
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.202
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.111
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.068
r_chiral_restr_other	0.065
r_symmetry_xyhbond_nbd_other	0.056
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5264
Nucleic Acid Atoms
Solvent Atoms	653
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing