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Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 6.5 298.15 25% PEG 3350, 0.2 M Ammonium Sulfate, 200 mM Bis Tris Propane pH 6.5, microbatch under oil, temperature 298.15K
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.73 α = 90 b = 77.73 β = 90 c = 224.54 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 IMAGE PLATE RIGAKU 2011-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 74.8 98.4 46337 45596 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LU1 2.6 74.8 2 43276 43276 2307 98.28 0.2196 0.2196 0.21686 0.2699 0.2652 RANDOM 41.547
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] 0.5 0.25 0.5 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.893 r_dihedral_angle_3_deg 16.295 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_1_deg 5.316 r_scangle_it 1.609 r_angle_refined_deg 1.168 r_scbond_it 0.967 r_mcangle_it 0.698 r_mcbond_it 0.367 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.893 r_dihedral_angle_3_deg 16.295 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_1_deg 5.316 r_scangle_it 1.609 r_angle_refined_deg 1.168 r_scbond_it 0.967 r_mcangle_it 0.698 r_mcbond_it 0.367 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10724 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 300
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling