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Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with biantennary pentasaccharide M592
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 8.0,
0.3 M Li2SO4,
30 % (w/v) PEG 3350,
10 % (v/v) ethylene glycol
wXHPcQHrME
Crystal Properties Matthews coefficient Solvent content 2.16 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.28 α = 108.81 b = 67.37 β = 92.2 c = 91.05 γ = 106.72
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M-F 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.6 42.52 96.2 0.054 0.034 0.999 10.4 3.5 125194
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 1.162 0.722 0.524 1.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5zic 1.6 42.52 125193 3770 96.191 0.185 0.1841 0.1842 0.2145 0.2146 34.716
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] -0.394 1.502 -0.052 2.302 -0.13 -2.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.234 r_dihedral_angle_4_deg 18.091 r_dihedral_angle_3_deg 14.646 r_lrange_it 8.288 r_lrange_other 8.258 r_dihedral_angle_1_deg 6.756 r_scangle_it 6.605 r_scangle_other 6.603 r_scbond_it 4.24 r_mcangle_it 4.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.234 r_dihedral_angle_4_deg 18.091 r_dihedral_angle_3_deg 14.646 r_lrange_it 8.288 r_lrange_other 8.258 r_dihedral_angle_1_deg 6.756 r_scangle_it 6.605 r_scangle_other 6.603 r_scbond_it 4.24 r_mcangle_it 4.224 r_mcangle_other 4.224 r_scbond_other 4.219 r_mcbond_it 2.888 r_mcbond_other 2.888 r_angle_refined_deg 1.62 r_angle_other_deg 1.291 r_nbd_other 0.242 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.167 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_1 0.087 r_xyhbond_nbd_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7738 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing