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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, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP at pH 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Protein 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 HEPPS (pH 8)
Crystal Properties Matthews coefficient Solvent content 2.34 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.788 α = 90 b = 128.158 β = 112.54 c = 58.475 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 2023-03-11 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 50 98.9 0.09 12.1 6.4 51464
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 2.1 96.6 0.44 2 3.3
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 40.59 48754 2710 98.88 0.18557 0.18294 0.1913 0.23393 0.2364 RANDOM 28.626
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] -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.276 r_dihedral_angle_2_deg 11.517 r_dihedral_angle_1_deg 6.715 r_long_range_B_refined 6.58 r_long_range_B_other 6.555 r_scangle_other 5.144 r_mcangle_it 3.907 r_mcangle_other 3.906 r_scbond_it 3.325 r_scbond_other 3.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.276 r_dihedral_angle_2_deg 11.517 r_dihedral_angle_1_deg 6.715 r_long_range_B_refined 6.58 r_long_range_B_other 6.555 r_scangle_other 5.144 r_mcangle_it 3.907 r_mcangle_other 3.906 r_scbond_it 3.325 r_scbond_other 3.316 r_mcbond_it 2.649 r_mcbond_other 2.644 r_angle_refined_deg 1.597 r_angle_other_deg 0.546 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 5665 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling REFMAC phasing