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STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMPOUND WBX09
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18% PEG 3350
0.2 M Na Malonate
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.147 α = 90 b = 110.205 β = 90 c = 135.411 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS EIGER2 S 16M 2023-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.7098 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 0.95 57.76 99.4 1 76.5 40 415408
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 0.33
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.95 57.755 408081 2000 94.531 0.181 0.1811 0.1811 0.189 0.1892 15.018
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] -0.327 0.286 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.222 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 8.479 r_dihedral_angle_1_deg 5.907 r_lrange_it 4.459 r_scangle_it 3.399 r_scbond_it 2.507 r_angle_refined_deg 2.105 r_mcangle_it 1.921 r_mcbond_it 1.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.222 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 8.479 r_dihedral_angle_1_deg 5.907 r_lrange_it 4.459 r_scangle_it 3.399 r_scbond_it 2.507 r_angle_refined_deg 2.105 r_mcangle_it 1.921 r_mcbond_it 1.329 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.124 r_ncsr_local_group_1 0.124 r_bond_refined_d 0.012 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5282 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2.multiplex data scaling PHASER phasing