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The structure of C100A mutant of Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NADH and UDP-D-glucuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 298 0.8 M sodium phosphate, 0.8 M potassium phosphate, and 0.1 M sodium-HEPES (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 4.51 72.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.564 α = 90 b = 144.564 β = 90 c = 130.519 γ = 120
Symmetry Space Group P 32 2 1
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 2M 2017-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000040 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.47 48.44 99.8 0.151 0.998 13.1 8.3 20833
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.47 3.8 99.2 0.8 0.844 1.9 7.9
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 6H0N 3.47 48.44 19736 1073 99.83 0.19806 0.19589 0.2034 0.23904 0.2438 RANDOM 124.459
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] 3.36 1.68 3.36 -10.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.346 r_dihedral_angle_4_deg 23.66 r_dihedral_angle_3_deg 18.101 r_long_range_B_refined 14.052 r_long_range_B_other 14.028 r_scangle_other 11.266 r_mcangle_it 10.597 r_mcangle_other 10.596 r_dihedral_angle_1_deg 8.131 r_scbond_it 7.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.346 r_dihedral_angle_4_deg 23.66 r_dihedral_angle_3_deg 18.101 r_long_range_B_refined 14.052 r_long_range_B_other 14.028 r_scangle_other 11.266 r_mcangle_it 10.597 r_mcangle_other 10.596 r_dihedral_angle_1_deg 8.131 r_scbond_it 7.501 r_scbond_other 7.5 r_mcbond_it 7.024 r_mcbond_other 7.023 r_angle_refined_deg 2.23 r_angle_other_deg 1.372 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.003 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 5725 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing