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Structure of UDP-Galactose-4-epimerase (GalE) bound to fragment from Diamond XChem experiment.
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 7.5 298 18% PEG 3350
0.2 M Sodium Malonate
Crystal Properties Matthews coefficient Solvent content 2.24 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.144 α = 90 b = 108.327 β = 90 c = 137.447 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 PILATUS 6M-F mirrors 2023-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 .7838 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.65 43.72 99.4 0.44 0.473 0.173 0.987 6.1 7.3 160447
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.27 8.289 8.9 3.223 0.071 0.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.651 43.72 83318 4221 99.597 0.191 0.1896 0.1896 0.2188 0.2188 23.482
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] -1.258 1.119 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.302 r_dihedral_angle_3_deg 12.9 r_dihedral_angle_2_deg 10.649 r_lrange_it 6.234 r_dihedral_angle_1_deg 5.761 r_scangle_it 4.698 r_scbond_it 3.181 r_mcangle_it 2.571 r_mcbond_it 1.839 r_angle_refined_deg 1.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.302 r_dihedral_angle_3_deg 12.9 r_dihedral_angle_2_deg 10.649 r_lrange_it 6.234 r_dihedral_angle_1_deg 5.761 r_scangle_it 4.698 r_scbond_it 3.181 r_mcangle_it 2.571 r_mcbond_it 1.839 r_angle_refined_deg 1.647 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.193 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.108 r_ncsr_local_group_1 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5270 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing