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Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, G233A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EK6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 20-22% (w/v) PEG3350 and 0.16-0.18 M magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.49 α = 90 b = 109.243 β = 90 c = 130.627 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2022-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99988 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 49.12 100 0.132 0.054 0.994 9.4 6.9 34777 30.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 100 0.624 0.257 0.844 3.1 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1EK6 2.25 49.12 32954 1794 99.94 0.17148 0.16841 0.22764 0.2366 RANDOM 35.258
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] 1.68 -1.94 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.53 r_dihedral_angle_2_deg 13.042 r_long_range_B_other 7.949 r_long_range_B_refined 7.945 r_dihedral_angle_1_deg 6.827 r_scangle_other 6.567 r_scbond_it 4.405 r_scbond_other 4.404 r_mcangle_it 4.316 r_mcangle_other 4.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.53 r_dihedral_angle_2_deg 13.042 r_long_range_B_other 7.949 r_long_range_B_refined 7.945 r_dihedral_angle_1_deg 6.827 r_scangle_other 6.567 r_scbond_it 4.405 r_scbond_other 4.404 r_mcangle_it 4.316 r_mcangle_other 4.315 r_mcbond_it 2.998 r_mcbond_other 2.998 r_angle_refined_deg 1.568 r_angle_other_deg 0.528 r_chiral_restr 0.073 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 5245 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing