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Caenorhabditis Elegans UDP-Glucose Dehydrogenase in complex with UDP-Xylose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10 mg/mL C. Elegans UDP-Glucose Dehydrogenase
Citric acid buffer pH 5.0
200mM Lithium Chloride
4% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.04 59.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.71 α = 90 b = 168.17 β = 90 c = 279.56 γ = 90
Symmetry Space Group P 2 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 80 CCD RAYONIX MX300HE 2017-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.449 52.698 98.1 0.996 9.1 6.295 266791
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.449 2.51 0.455
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2O3J 2.449 52.698 1.34 266577 1847 98.08 0.1937 0.1935 0.1942 0.2204 0.2209
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.432 f_angle_d 0.911 f_chiral_restr 0.063 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42852 Nucleic Acid Atoms Solvent Atoms 1194 Heterogen Atoms 816
Software Software Software Name Purpose PHENIX refinement XDS data scaling Coot model building PHENIX phasing XDS data reduction