☰ Navigation Tabs
Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation
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 1.55 20.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47 α = 108.36 b = 68.17 β = 92.28 c = 90.99 γ = 106.86
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 2019-01-22 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 1.9 43.31 97 0.066 0.042 0.997 9.9 3.5 77533
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 1.9 1.95 1.159 0.721 0.422 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 1.9 43.31 77533 3684 96.94 0.196 0.1941 0.1941 0.2371 0.2371 46.468
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] -0.211 0.557 0.304 1.185 1.592 -2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.22 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_3_deg 14.703 r_lrange_it 7.646 r_lrange_other 7.624 r_dihedral_angle_1_deg 6.834 r_scangle_it 6.132 r_scangle_other 6.113 r_mcangle_it 4.795 r_mcangle_other 4.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.22 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_3_deg 14.703 r_lrange_it 7.646 r_lrange_other 7.624 r_dihedral_angle_1_deg 6.834 r_scangle_it 6.132 r_scangle_other 6.113 r_mcangle_it 4.795 r_mcangle_other 4.794 r_scbond_it 4.163 r_scbond_other 4.132 r_mcbond_it 3.599 r_mcbond_other 3.598 r_angle_refined_deg 1.457 r_angle_other_deg 1.252 r_symmetry_nbd_refined 0.206 r_nbd_refined 0.199 r_nbd_other 0.195 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.115 r_ncsr_local_group_1 0.088 r_symmetry_xyhbond_nbd_other 0.084 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.071 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 7989 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing