☰ Navigation Tabs
Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP-2-deoxy-2-fluoroglucose 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 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.52 α = 108.42 b = 69.21 β = 92.25 c = 90.65 γ = 106.54
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 2019-05-19 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 44.14 94.7 0.044 0.028 0.999 11.1 3.5 106002
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 1.085 0.705 0.547 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5zic 1.7 44.14 106001 3663 94.657 0.177 0.1754 0.2115 0.2311 43.149
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] -2.177 0.272 -0.545 1.371 1.706 -0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 17.603 r_dihedral_angle_3_deg 15.265 r_lrange_other 8.394 r_lrange_it 8.392 r_dihedral_angle_1_deg 7.07 r_scangle_other 6.572 r_scangle_it 6.569 r_mcangle_it 4.733 r_mcangle_other 4.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 17.603 r_dihedral_angle_3_deg 15.265 r_lrange_other 8.394 r_lrange_it 8.392 r_dihedral_angle_1_deg 7.07 r_scangle_other 6.572 r_scangle_it 6.569 r_mcangle_it 4.733 r_mcangle_other 4.733 r_scbond_it 4.312 r_scbond_other 4.299 r_mcbond_it 3.457 r_mcbond_other 3.456 r_angle_refined_deg 1.588 r_angle_other_deg 1.274 r_symmetry_nbd_refined 0.233 r_nbd_other 0.225 r_symmetry_xyhbond_nbd_refined 0.209 r_nbd_refined 0.202 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.163 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.072 r_bond_refined_d 0.009 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 8127 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing