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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 protein 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 coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.34 α = 90 b = 128.608 β = 111.24 c = 58.934 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 2023-01-27 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 2.1 50 99.1 0.082 14.7 7.9 45153
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) Redundancy Number Unique Reflections (All) 1 2.1 2.2 96.9 0.36 2.7 3.5
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.1 40.67 42938 2215 99.13 0.18286 0.18038 0.1874 0.23067 0.2342 RANDOM 25.943
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 -0.01 0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.616 r_dihedral_angle_2_deg 9.348 r_long_range_B_refined 6.871 r_long_range_B_other 6.87 r_dihedral_angle_1_deg 6.687 r_scangle_other 5.325 r_mcangle_other 3.63 r_mcangle_it 3.629 r_scbond_it 3.326 r_scbond_other 3.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.616 r_dihedral_angle_2_deg 9.348 r_long_range_B_refined 6.871 r_long_range_B_other 6.87 r_dihedral_angle_1_deg 6.687 r_scangle_other 5.325 r_mcangle_other 3.63 r_mcangle_it 3.629 r_scbond_it 3.326 r_scbond_other 3.325 r_mcbond_it 2.392 r_mcbond_other 2.389 r_angle_refined_deg 1.624 r_angle_other_deg 0.547 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 5676 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling REFMAC phasing