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A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (alpha-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - Unliganded alpha-3GalT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 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 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.947 α = 90 b = 66.293 β = 102.59 c = 83.933 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 PILATUS 6M-F 2017-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 1.7 81.91 100 0.0809 0.998 10.11 3.3 79440
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 1.7 1.76 100 0.9901 0.424 3.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1O7Q 1.7 81.91 79319 7425 94.81 0.189 0.1872 0.1892 0.2234 0.2259
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 13.505 f_angle_d 1.035 f_chiral_restr 0.063 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4542 Nucleic Acid Atoms Solvent Atoms 697 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data scaling XDS data reduction