8QC2

Crystal structure of NAD-dependent glycoside hydrolase from Flavobacterium sp. (strain K172) in complex with co-factor NAD+ and sulfoquinovose (SQ)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AF-A0A7D7VZ79-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	100 mM bis-tris propane pH 7, 0.02 mM sodium and potassium phosphate, 28% (w/v) PEG3350, 5 mM NAD+ and 1 mM manganese chloride. SQ powder soaked into the well directly for around 2 minutes

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.517	α = 90
b = 160.381	β = 90
c = 185.749	γ = 90

Symmetry
Space Group	C 2 2 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		2023-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.3	51.19	100	0.288	0.299	0.08	0.995	6.2	13.8		73391

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.35		100	1.616	1.675	0.438	0.876		14.4

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	2.3	49.06	69673	3609	99.86	0.19748	0.19499	0.24593	RANDOM	29.867

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]
-0.08			-3.47		3.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.504
r_dihedral_angle_2_deg	12.194
r_long_range_B_refined	7.138
r_long_range_B_other	7.138
r_dihedral_angle_1_deg	7.023
r_scangle_other	5.966
r_mcangle_it	4.298
r_mcangle_other	4.298
r_scbond_it	3.832
r_scbond_other	3.831
r_mcbond_it	2.875
r_mcbond_other	2.874
r_angle_refined_deg	1.428
r_angle_other_deg	0.484
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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	11072
Nucleic Acid Atoms
Solvent Atoms	740
Heterogen Atoms	284

Software

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