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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 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SY9
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.
Precipitant used was 18-22% poly(ethylene glycol) 8000, 100 mM CHES (pH 9)
Crystal Properties Matthews coefficient Solvent content 2.35 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.088 α = 90 b = 129.986 β = 112.61 c = 58.613 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 2023-03-20 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 2.3 50 99.6 0.096 9.7 8.5 34302
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 2.3 2.4 98.8 0.45 2.2 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.3 44.79 32597 1705 99.65 0.20395 0.20187 0.24327 0.2135 RANDOM 29.641
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] 2.66 1.09 -1.94 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.237 r_dihedral_angle_2_deg 9.792 r_dihedral_angle_1_deg 7.055 r_long_range_B_refined 7.011 r_long_range_B_other 7.001 r_scangle_other 5.075 r_mcangle_it 3.943 r_mcangle_other 3.943 r_scbond_it 3.078 r_scbond_other 3.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.237 r_dihedral_angle_2_deg 9.792 r_dihedral_angle_1_deg 7.055 r_long_range_B_refined 7.011 r_long_range_B_other 7.001 r_scangle_other 5.075 r_mcangle_it 3.943 r_mcangle_other 3.943 r_scbond_it 3.078 r_scbond_other 3.073 r_mcbond_it 2.445 r_mcbond_other 2.443 r_angle_refined_deg 1.49 r_angle_other_deg 0.49 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 5671 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling REFMAC phasing