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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
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 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.03 α = 107.77 b = 69.59 β = 91.81 c = 90 γ = 106.94
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 2019-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.7 43.43 96 0.047 0.03 0.999 9.9 3.6 108811
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 1.7 1.74 1.346 0.804 0.562 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 1.7 43.43 104711 3727 95.643 0.186 0.1845 0.189 0.2228 0.2253 54.886
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] -3.17 1.476 1.511 1.744 3.277 -2.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.194 r_dihedral_angle_4_deg 16.022 r_dihedral_angle_3_deg 14.595 r_lrange_other 9.344 r_lrange_it 9.335 r_scangle_it 7.598 r_scangle_other 7.594 r_dihedral_angle_1_deg 7.055 r_mcangle_other 5.608 r_mcangle_it 5.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.194 r_dihedral_angle_4_deg 16.022 r_dihedral_angle_3_deg 14.595 r_lrange_other 9.344 r_lrange_it 9.335 r_scangle_it 7.598 r_scangle_other 7.594 r_dihedral_angle_1_deg 7.055 r_mcangle_other 5.608 r_mcangle_it 5.607 r_scbond_it 5.149 r_scbond_other 5.121 r_mcbond_it 4.187 r_mcbond_other 4.182 r_angle_refined_deg 1.536 r_angle_other_deg 1.255 r_nbd_other 0.228 r_symmetry_xyhbond_nbd_refined 0.206 r_symmetry_nbd_refined 0.194 r_nbd_refined 0.192 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.154 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8218 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing