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Crystal structure of MGAT5 bump-and-hole mutant in complex with UDP and M592
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 15-20% PEG3350, 0.1M Tris-HCl pH 8-8.5, 0.3M Li2SO4, 0-10% ethylene glycol, Microseed matrix screening
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.507 α = 108.208 b = 69.069 β = 92.088 c = 90.993 γ = 106.747
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 EIGER2 XE 16M 2023-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.72738 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.97 44.1 94.4 0.116 0.164 0.116 0.994 6.6 3.8 68392
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.01 1.557 2.2 1.554 0.27 3.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.97 44.1 68300 3266 94.644 0.202 0.1996 0.2418 0.2042 38.744
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] 0.475 -0.48 -1.014 0.507 0.172 -0.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.255 r_dihedral_angle_3_deg 14.72 r_dihedral_angle_2_deg 13.407 r_dihedral_angle_1_deg 7.351 r_lrange_it 6.435 r_lrange_other 6.424 r_scangle_it 4.219 r_scangle_other 4.196 r_mcangle_it 3.796 r_mcangle_other 3.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.255 r_dihedral_angle_3_deg 14.72 r_dihedral_angle_2_deg 13.407 r_dihedral_angle_1_deg 7.351 r_lrange_it 6.435 r_lrange_other 6.424 r_scangle_it 4.219 r_scangle_other 4.196 r_mcangle_it 3.796 r_mcangle_other 3.795 r_scbond_it 2.748 r_scbond_other 2.732 r_mcbond_it 2.458 r_mcbond_other 2.458 r_angle_refined_deg 2.139 r_angle_other_deg 0.746 r_xyhbond_nbd_refined 0.315 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.194 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.177 r_nbd_other 0.171 r_ncsr_local_group_1 0.108 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8018 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing