☰ Navigation Tabs
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 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid.
Precipitant solution: 22-27% pentaerythritol propoxylate (5/4 PO/OH), 100 mM homopipes (pH 5)
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.455 α = 90 b = 128.796 β = 111.09 c = 58.663 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 2022-12-16 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 1.8 50 99 0.056 17.5 7.4 71545
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 1.8 1.9 98.7 0.3 3.5 4.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.8 41.71 68030 3515 99.01 0.1815 0.1796 0.1879 0.21819 0.2249 RANDOM 20.549
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.369 r_dihedral_angle_2_deg 9.049 r_long_range_B_refined 6.406 r_long_range_B_other 6.331 r_dihedral_angle_1_deg 6.194 r_scangle_other 4.55 r_mcangle_it 3.031 r_mcangle_other 3.03 r_scbond_other 2.819 r_scbond_it 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.369 r_dihedral_angle_2_deg 9.049 r_long_range_B_refined 6.406 r_long_range_B_other 6.331 r_dihedral_angle_1_deg 6.194 r_scangle_other 4.55 r_mcangle_it 3.031 r_mcangle_other 3.03 r_scbond_other 2.819 r_scbond_it 2.816 r_mcbond_it 1.973 r_mcbond_other 1.973 r_angle_refined_deg 1.563 r_angle_other_deg 0.531 r_chiral_restr 0.076 r_bond_refined_d 0.008 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 5643 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing