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Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in complex with isopropyl dodec-11-enylfluorophosphonate (IDFP) and a small molecule activator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.25 M lithium sulfate, 0.1 M Tris pH 8.5, and 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.93 68.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.697 α = 90 b = 106.377 β = 125.45 c = 117.823 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 300 mm CCD 2016-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.1 30 98.9 0.115 11.1 4.2 24440
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 3.1 3.15 100 0.55 1.27 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5TXF 3.1 28.8 20413 1145 87.26 0.19508 0.19252 0.1975 0.23932 0.2403 RANDOM 70.341
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] -0.42 -0.23 1.1 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_3_deg 16.686 r_dihedral_angle_4_deg 15.087 r_dihedral_angle_1_deg 7.215 r_long_range_B_refined 6.294 r_long_range_B_other 6.292 r_mcangle_it 3.784 r_mcangle_other 3.783 r_scangle_other 3.664 r_mcbond_it 2.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_3_deg 16.686 r_dihedral_angle_4_deg 15.087 r_dihedral_angle_1_deg 7.215 r_long_range_B_refined 6.294 r_long_range_B_other 6.292 r_mcangle_it 3.784 r_mcangle_other 3.783 r_scangle_other 3.664 r_mcbond_it 2.246 r_mcbond_other 2.246 r_scbond_it 2.137 r_scbond_other 2.131 r_angle_refined_deg 1.331 r_angle_other_deg 0.822 r_chiral_restr 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5978 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing