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STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMPOUND WBX04
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 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.358 α = 90 b = 46.3 β = 90 c = 110.727 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 XE 9M 2023-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
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 1.37 68.272 97.4 0.96 12.5 73.3 143992
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 1.37 1.39 0.41
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 1.37 68.272 143611 7068 97.095 0.156 0.1538 0.1609 0.1897 0.192 21.462
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] 0.203 0.745 -0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.543 r_dihedral_angle_3_deg 11.624 r_lrange_it 11.364 r_lrange_other 11.364 r_dihedral_angle_2_deg 9.557 r_scangle_it 8.795 r_scangle_other 8.794 r_mcangle_it 6.803 r_mcangle_other 6.803 r_scbond_it 6.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.543 r_dihedral_angle_3_deg 11.624 r_lrange_it 11.364 r_lrange_other 11.364 r_dihedral_angle_2_deg 9.557 r_scangle_it 8.795 r_scangle_other 8.794 r_mcangle_it 6.803 r_mcangle_other 6.803 r_scbond_it 6.263 r_scbond_other 6.259 r_dihedral_angle_1_deg 6.115 r_mcbond_it 4.822 r_mcbond_other 4.813 r_dihedral_angle_other_2_deg 4.46 r_rigid_bond_restr 3.667 r_angle_refined_deg 1.719 r_angle_other_deg 0.613 r_nbd_refined 0.211 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.15 r_symmetry_nbd_refined 0.114 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5311 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing