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The extra-helical binding site of GPR40 and the structural basis for allosteric agonism and incretin stimulation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 298 0.1 M Tris HCl, pH 8.5, 30% PEG 400, 0.2 M ammonium formate.
Crystal Properties Matthews coefficient Solvent content 3.12 60.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.654 α = 90 b = 55.95 β = 93.77 c = 80.313 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 RAYONIX MX-225 2016-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.76 19.81 99.6 0.13 5.9 3.7 16090
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.91 100 1.2 3.7
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 4PHU 2.76 19.81 16090 857 100 0.2326 0.2304 0.2309 0.2727 0.2756 RANDOM 41.374
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] 0.77 -1.55 3.1 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_dihedral_angle_3_deg 15.338 r_dihedral_angle_4_deg 12.2 r_dihedral_angle_1_deg 3.932 r_angle_refined_deg 0.952 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3128 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing