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The structure of wild-type Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NAD+ and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SLG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M sodium-HEPES
Crystal Properties Matthews coefficient Solvent content 4.79 74.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.028 α = 90 b = 146.028 β = 90 c = 132.845 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-F 2017-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.003680 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 3.02 126.46 98.9 0.146 0.992 9.2 4.4 32264
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 3.02 3.18 95.4 0.8 0.378 1 4.5
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 3SLG 3.02 126.46 30595 1640 98.84 0.20944 0.20711 0.2163 0.25278 0.2543 RANDOM 77.855
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] 1.54 0.77 1.54 -5.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.309 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 17.064 r_long_range_B_refined 10.782 r_long_range_B_other 10.782 r_scangle_other 8.85 r_mcangle_it 7.935 r_mcangle_other 7.934 r_dihedral_angle_1_deg 7.363 r_scbond_it 5.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.309 r_dihedral_angle_4_deg 20.381 r_dihedral_angle_3_deg 17.064 r_long_range_B_refined 10.782 r_long_range_B_other 10.782 r_scangle_other 8.85 r_mcangle_it 7.935 r_mcangle_other 7.934 r_dihedral_angle_1_deg 7.363 r_scbond_it 5.83 r_scbond_other 5.83 r_mcbond_it 5.408 r_mcbond_other 5.407 r_angle_refined_deg 1.824 r_angle_other_deg 1.076 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5840 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing