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Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain.
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 Citrate pH 5.0
16% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.809 α = 90 b = 100.415 β = 90 c = 207.981 γ = 90
Symmetry Space Group P 21 21 21
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 2018-03-10 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 2.198 48.81 93.4 0.122 0.047 0.998 12.3 7.8 36979
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 2.2 2.49 1.223 0.479 0.615 1.7
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 2.198 48.81 35113 1866 57.085 0.211 0.2081 0.2082 0.2625 0.2626 70.676
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] -2.517 10.152 -7.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.424 r_dihedral_angle_4_deg 18.034 r_dihedral_angle_3_deg 17.643 r_lrange_it 7.371 r_lrange_other 7.369 r_dihedral_angle_1_deg 7.238 r_scangle_it 5.548 r_scangle_other 5.547 r_mcangle_it 4.779 r_mcangle_other 4.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.424 r_dihedral_angle_4_deg 18.034 r_dihedral_angle_3_deg 17.643 r_lrange_it 7.371 r_lrange_other 7.369 r_dihedral_angle_1_deg 7.238 r_scangle_it 5.548 r_scangle_other 5.547 r_mcangle_it 4.779 r_mcangle_other 4.779 r_scbond_it 3.52 r_scbond_other 3.52 r_mcbond_it 3.181 r_mcbond_other 3.18 r_angle_refined_deg 1.572 r_angle_other_deg 1.246 r_symmetry_xyhbond_nbd_refined 0.311 r_nbd_other 0.232 r_nbd_refined 0.214 r_symmetry_xyhbond_nbd_other 0.208 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7886 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing