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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 3D fragment 2548
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YJT same protein with a different ligand
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 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.86 α = 107.3 b = 68.54 β = 92.16 c = 91.31 γ = 107.05
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 EIGER X 16M 2019-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.89 60.47 97.26 0.047 1 13.6 3.5 80017
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 1.297 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.89 60.465 80017 3795 97.259 0.192 0.1897 0.1979 0.2327 0.2393 54.819
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] -0.258 1.025 0.567 -0.062 1.78 -1.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.501 r_dihedral_angle_3_deg 15.187 r_lrange_it 10.513 r_lrange_other 10.512 r_scangle_it 9.087 r_scangle_other 9.087 r_dihedral_angle_1_deg 6.898 r_mcangle_it 6.839 r_mcangle_other 6.839 r_scbond_it 6.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.501 r_dihedral_angle_3_deg 15.187 r_lrange_it 10.513 r_lrange_other 10.512 r_scangle_it 9.087 r_scangle_other 9.087 r_dihedral_angle_1_deg 6.898 r_mcangle_it 6.839 r_mcangle_other 6.839 r_scbond_it 6.459 r_scbond_other 6.459 r_dihedral_angle_2_deg 6.242 r_mcbond_it 5.456 r_mcbond_other 5.456 r_angle_refined_deg 1.51 r_angle_other_deg 0.487 r_xyhbond_nbd_refined 0.265 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.197 r_nbd_other 0.19 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.176 r_symmetry_xyhbond_nbd_other 0.137 r_ncsr_local_group_1 0.102 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.074 r_gen_planes_refined 0.009 r_bond_refined_d 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 8033 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing