☰ Navigation Tabs
Crystal structure of human MGAT1 in complex with UDP-GlcNAc.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ZAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 16% PEG 4000, 100 mM Tris-HCl (pH 8.5), and 200 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.925 α = 90 b = 113.052 β = 90 c = 129.542 γ = 90
Symmetry Space Group P 2 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 EIGER X 9M 2022-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.93925 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 49.4 100 0.167 0.188 0.994 8.8 8.6 55419 24.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.966 1.106 0.758 2.3 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 49.4 1.35 55348 2801 99.96 0.172 0.1695 0.1694 0.2197 0.2197 25.43
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.1821 f_angle_d 0.8928 f_chiral_restr 0.0546 f_plane_restr 0.0093 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5635 Nucleic Acid Atoms Solvent Atoms 707 Heterogen Atoms 80
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction Aimless data scaling REFMAC phasing