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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, apo form, pH 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 8-12% poly(ethylene glycol) 8000,
1 M NMe4Cl, 100 mM CHES (pH9)
Crystal Properties Matthews coefficient Solvent content 2.89 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.675 α = 90 b = 88.926 β = 98.79 c = 87.567 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 2022-12-28 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 98.7 0.081 13 8.6 41084
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 96.2 0.45 2.6 4.7
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 MOLECULAR REPLACEMENT THROUGHOUT 2.3 46.07 39026 2058 98.75 0.2015 0.19847 0.25908 0.2275 RANDOM 38.239
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 Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.487 r_long_range_B_refined 8.919 r_long_range_B_other 8.915 r_dihedral_angle_2_deg 8.765 r_dihedral_angle_1_deg 7.019 r_scangle_other 6.635 r_mcangle_it 5.832 r_mcangle_other 5.831 r_scbond_it 4.165 r_scbond_other 4.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.487 r_long_range_B_refined 8.919 r_long_range_B_other 8.915 r_dihedral_angle_2_deg 8.765 r_dihedral_angle_1_deg 7.019 r_scangle_other 6.635 r_mcangle_it 5.832 r_mcangle_other 5.831 r_scbond_it 4.165 r_scbond_other 4.165 r_mcbond_it 3.739 r_mcbond_other 3.739 r_angle_refined_deg 1.506 r_angle_other_deg 0.502 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 5700 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing