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A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - a3GalT in complex with lactose - a3GalT-LAT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.010 M beta-lactose, 0.02 M L-Na-glutamate, 0.02 M alanine (racemic), 0.02 M glycine, 0.02 M L-lysine (racemic), 0.02 M serine (racemic), 0.1 M Sodium HEPES-MOPS (acid) mix pH 7.5, 20% (v/v) glycerol and 10% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.66 α = 90 b = 67.47 β = 119.33 c = 97.89 γ = 90
Symmetry Space Group C 1 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 PILATUS3 6M 2017-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.98 42.67 98 0.047 0.999 12.67 3.4 51440
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 1.98 2.05 99 0.5436 0.786 1.93 3.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NR9 1.98 57.391 0.15 92946 4753 90.86 0.198 0.196 0.1995 0.236 0.2397 Random
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 19.9 f_angle_d 1.05 f_chiral_restr 0.062 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4495 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing