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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 UDP and 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
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.6 α = 107.48 b = 69.55 β = 92.26 c = 90.94 γ = 106.22
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 2019-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95004 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 1.96 85.95 95.5 0.055 0.035 0.999 12.8 3.5 71053
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 1.96 2.01 1.244 0.791 0.581 1.1
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 1.96 85.95 71053 3368 95.437 0.202 0.1999 0.2 0.2523 0.2523 51.702
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] -2.859 0.183 0.84 2.288 3.094 -2.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.377 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 15.991 r_lrange_it 8.796 r_lrange_other 8.796 r_scangle_it 7.235 r_scangle_other 7.199 r_dihedral_angle_1_deg 7.139 r_mcangle_it 5.965 r_mcangle_other 5.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.377 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 15.991 r_lrange_it 8.796 r_lrange_other 8.796 r_scangle_it 7.235 r_scangle_other 7.199 r_dihedral_angle_1_deg 7.139 r_mcangle_it 5.965 r_mcangle_other 5.964 r_scbond_it 5.14 r_scbond_other 5.092 r_mcbond_it 4.489 r_mcbond_other 4.489 r_angle_refined_deg 1.597 r_angle_other_deg 1.261 r_symmetry_nbd_refined 0.224 r_nbd_other 0.214 r_nbd_refined 0.204 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.138 r_ncsr_local_group_1 0.084 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8103 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing