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Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, I160L/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 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.228 α = 90 b = 108.929 β = 90 c = 130.862 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 2.6 49.11 99.9 0.207 0.085 0.976 5.9 6.8 22589 26.84
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 2.6 2.72 99.9 0.633 0.257 0.852 3.4 7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EK6 2.6 49.11 21392 1144 99.68 0.17582 0.17222 0.1793 0.24423 0.2423 RANDOM 33.444
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] 0.56 -0.26 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.508 r_dihedral_angle_2_deg 10.147 r_dihedral_angle_1_deg 7.686 r_long_range_B_refined 7.675 r_long_range_B_other 7.674 r_scangle_other 5.886 r_mcangle_it 4.545 r_mcangle_other 4.544 r_scbond_it 3.72 r_scbond_other 3.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.508 r_dihedral_angle_2_deg 10.147 r_dihedral_angle_1_deg 7.686 r_long_range_B_refined 7.675 r_long_range_B_other 7.674 r_scangle_other 5.886 r_mcangle_it 4.545 r_mcangle_other 4.544 r_scbond_it 3.72 r_scbond_other 3.697 r_mcbond_it 2.902 r_mcbond_other 2.901 r_angle_refined_deg 1.557 r_angle_other_deg 0.516 r_chiral_restr 0.073 r_bond_refined_d 0.007 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 5270 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing