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Crystal structure of human MGAT1 in complex with TNG-9333.
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 7 293 0.2 M triammonium citrate (pH 7.0), 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.833 α = 90 b = 111.031 β = 90 c = 138.9 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 16M 2024-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.999 SPring-8 BL45XU
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 49.16 100 0.171 0.186 0.998 17.2 12.6 58243 25.51
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 1.065 1.153 0.921 3.8 13.1
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 (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 46.35 58175 2887 99.97 0.1733 0.1715 0.1715 0.2077 0.2075 33.98
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 6.4704 f_angle_d 0.6135 f_chiral_restr 0.0465 f_plane_restr 0.0057 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5297 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction Aimless data scaling REFMAC phasing