8SYD

X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP-N-acetylglucosamine at pH 6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	Protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and 5 mM UDP-N-acetylglucosamine. Precipitant used was 22-27% pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES (pH 6)

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.272	α = 90
b = 128.436	β = 114.06
c = 58.135	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	Bruker PHOTON II		2023-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	50	99.5	0.085	12.8	7.9		38022

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	97.9		0.38	3.2	3.7

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	FOURIER SYNTHESIS	THROUGHOUT	2.2	40.12	36200	1822	99.47	0.17517	0.17248	0.22914	RANDOM	16.035

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_3_deg	17.127
r_dihedral_angle_2_deg	8.251
r_dihedral_angle_1_deg	6.619
r_long_range_B_refined	4.855
r_long_range_B_other	4.836
r_scangle_other	3.594
r_mcangle_it	2.261
r_mcangle_other	2.261
r_scbond_other	2.177
r_scbond_it	2.175
r_angle_refined_deg	1.595
r_mcbond_it	1.362
r_mcbond_other	1.362
r_angle_other_deg	0.535
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
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	5747
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	166

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
REFMAC	phasing