8JJT

Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.153	15% PEG 20000, 0.1M Hepes/NaOH pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.223	α = 90
b = 56.375	β = 91.106
c = 108.445	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2023-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	SSRF	BL19U1

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	1.88	48.85	99.8	0.998	15.2	6.6		106627

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91			0.771

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.88	48.848	106588	4962	94.183	0.188	0.1865	0.2149	27.259

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]
3.959		6.614	-11.483		7.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.253
r_dihedral_angle_4_deg	19.133
r_dihedral_angle_3_deg	15.01
r_dihedral_angle_1_deg	7.183
r_lrange_it	6.479
r_lrange_other	6.345
r_scangle_it	4.698
r_scangle_other	4.697
r_mcangle_it	3.484
r_mcangle_other	3.484
r_scbond_it	3.316
r_scbond_other	3.315
r_mcbond_it	2.666
r_mcbond_other	2.666
r_angle_refined_deg	1.818
r_angle_other_deg	1.418
r_nbd_refined	0.207
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.183
r_xyhbond_nbd_refined	0.177
r_symmetry_xyhbond_nbd_other	0.175
r_nbtor_refined	0.155
r_nbd_other	0.138
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7223
Nucleic Acid Atoms
Solvent Atoms	810
Heterogen Atoms	117

Software

Software
Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	phasing