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Crystal structure of human MGAT1 in complex with UDP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AM3
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 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.373 α = 90 b = 112.62 β = 90 c = 128.486 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 CCD DECTRIS EIGER X 16M 2020-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U
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 1.55 48.96 99.5 0.059 0.068 0.998 21.3 7.6 114513 13.13
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 1.55 1.58 94.4 0.212 0.276 0.924 5.3 3.7
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 1.55 33.64 1.36 114414 5594 99.43 0.153 0.1517 0.1517 0.1768 0.1768 18.33
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 7.0277 f_angle_d 1.4804 f_chiral_restr 0.0925 f_bond_d 0.0167 f_plane_restr 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5546 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 70
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction Aimless data scaling REFMAC phasing