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Structure of the lipoprotein lipase GPIHBP1 complex that mediates plasma triglyceride hydrolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HPL PDB entry 1HPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM magnesium acetate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.948 α = 90 b = 153.206 β = 90 c = 95.783 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 PIXEL DECTRIS PILATUS3 6M Be CRL/Si elliptical mirror 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.000 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.8 95.8 99.4 0.01 0.985 13.5 3.3 37662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.7 0.53 0.728 1.5 3.2
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 PDB entry 1HPL 2.8 48.41 35568 1833 99.23 0.19738 0.19534 0.2068 0.23545 0.2435 RANDOM 94.934
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] 1.49 -3.01 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.007 r_dihedral_angle_4_deg 18.563 r_dihedral_angle_3_deg 18.225 r_dihedral_angle_1_deg 8.572 r_long_range_B_refined 7.556 r_long_range_B_other 7.556 r_scangle_other 3.567 r_mcangle_it 2.967 r_mcangle_other 2.967 r_scbond_it 2.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.007 r_dihedral_angle_4_deg 18.563 r_dihedral_angle_3_deg 18.225 r_dihedral_angle_1_deg 8.572 r_long_range_B_refined 7.556 r_long_range_B_other 7.556 r_scangle_other 3.567 r_mcangle_it 2.967 r_mcangle_other 2.967 r_scbond_it 2.088 r_scbond_other 2.088 r_mcbond_it 1.763 r_mcbond_other 1.762 r_angle_refined_deg 1.433 r_angle_other_deg 0.887 r_chiral_restr 0.131 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 7873 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing