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In meso structure of apolipoprotein N-acyltransferase, Lnt, from Escherichia coli in 7.10 monoacylglycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ACI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 100 mM MES pH 6.0, 8 %(v/v) MPD, and 50-400 mM sodium or potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.679 α = 90 b = 76.461 β = 90 c = 157.08 γ = 90
Symmetry Space Group P 21 2 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 EIGER2 X CdTe 9M 2021-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.19 46.5 99.1 0.99 7.7 6.4 30881 33.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.27 0.31
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.19 46.5 1.33 30740 1540 99.01 0.2009 0.1985 0.2458 0.2336 39.62
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 12.428 f_angle_d 0.7979 f_chiral_restr 0.0441 f_plane_restr 0.0091 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4026 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 216
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing