8SY0 | pdb_00008sy0

X-ray crystal structure of UDP- 2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27 in complex with its product UDP-2,3-diacetamido-2,3-dideoxy-d-mannuronic acid at pH 9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SXY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid 18-22% poly(ethylene glycol) 3350, 200 mM LiCl, 100 mM CHES (pH 9)
Crystal Properties
Matthews coefficientSolvent content
2.3748.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.34α = 90
b = 128.608β = 111.24
c = 58.934γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2023-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15099.10.08214.77.945153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.296.90.362.73.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.140.6742938221599.130.182860.180380.190.230670.23RANDOM25.943
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]
-0.04-0.010.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.616
r_dihedral_angle_2_deg9.348
r_long_range_B_refined6.871
r_long_range_B_other6.87
r_dihedral_angle_1_deg6.687
r_scangle_other5.325
r_mcangle_other3.63
r_mcangle_it3.629
r_scbond_it3.326
r_scbond_other3.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.616
r_dihedral_angle_2_deg9.348
r_long_range_B_refined6.871
r_long_range_B_other6.87
r_dihedral_angle_1_deg6.687
r_scangle_other5.325
r_mcangle_other3.63
r_mcangle_it3.629
r_scbond_it3.326
r_scbond_other3.325
r_mcbond_it2.392
r_mcbond_other2.389
r_angle_refined_deg1.624
r_angle_other_deg0.547
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms5676
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
REFMACphasing