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Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc
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 7.5 277.15 30% (v/v) PEG400, 0.2 M MgCl, 0.1 M HEPES-NaOH (pH 7.5), and 10 mM UDP-GlcNAc
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.45 α = 90 b = 69.45 β = 90 c = 321.986 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 100 0.124 28.2 16.9 32699
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.951 3.5 17
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 34.75 30845 1649 99.61 0.1832 0.1812 0.1919 0.2212 0.2284 RANDOM 33.788
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 r_dihedral_angle_2_deg 34.649 r_dihedral_angle_3_deg 13.619 r_dihedral_angle_4_deg 12.597 r_dihedral_angle_1_deg 7.03 r_angle_refined_deg 1.661 r_angle_other_deg 1.492 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_other 0.011 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_3_deg 13.619 r_dihedral_angle_4_deg 12.597 r_dihedral_angle_1_deg 7.03 r_angle_refined_deg 1.661 r_angle_other_deg 1.492 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2588 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing