8SYE | pdb_00008sye

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 at pH 6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SY9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and 5 mM UDP. Precipitant used was 22-27% pentaerythritol propoxylate (5/4 PO/OH), 100 mM MES (pH 6)
Crystal Properties
Matthews coefficientSolvent content
2.3347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.717α = 90
b = 128.061β = 112.61
c = 58.364γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2023-03-04MSINGLE 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
11.95097.50.09711.16.458879
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9286.80.442.42.3

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 SYNTHESISTHROUGHOUT1.941.2356098278197.480.200250.198630.210.231990.24RANDOM24.542
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.384
r_dihedral_angle_2_deg10.092
r_dihedral_angle_1_deg6.572
r_long_range_B_refined5.767
r_long_range_B_other5.736
r_scangle_other4.431
r_mcangle_it3.185
r_mcangle_other3.185
r_scbond_it2.807
r_scbond_other2.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.384
r_dihedral_angle_2_deg10.092
r_dihedral_angle_1_deg6.572
r_long_range_B_refined5.767
r_long_range_B_other5.736
r_scangle_other4.431
r_mcangle_it3.185
r_mcangle_other3.185
r_scbond_it2.807
r_scbond_other2.797
r_mcbond_it2.138
r_mcbond_other2.132
r_angle_refined_deg1.534
r_angle_other_deg0.523
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms5674
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
REFMACphasing