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Crystal structure of Glucagon-Like Peptide-1 in complex with the extracellular domain of the Glucagon-Like Peptide-1 Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C59 PDB entry 3C59 without ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 291 0.1M N-(2-Acetamido) Iminodiacetic Acid (ADA), pH 6.9, 14 vol-% (+/-)-2-Methyl-2,4-pentanediol (MPD), 9mM n-decyl-beta-D-thiomaltoside, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.67 α = 90 b = 42.67 β = 90 c = 95.09 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 CCD MARMOSAIC 225 mm CCD 2008-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0 MAX II I911-3
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 2.1 95 98 0.111 14 7 10585 10348 25.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 98 0.449 5.3 7 1132
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3C59 without ligand 2.1 28.53 8786 8357 429 97.85 0.18058 0.17816 0.1925 0.22622 0.2393 RANDOM 13.663
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] 2.61 -1.42 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.406 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_4_deg 13.082 r_dihedral_angle_1_deg 6.462 r_scangle_it 4.717 r_scbond_it 2.859 r_mcangle_it 1.885 r_angle_refined_deg 1.681 r_angle_other_deg 1.072 r_mcbond_it 1.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.406 r_dihedral_angle_3_deg 14.042 r_dihedral_angle_4_deg 13.082 r_dihedral_angle_1_deg 6.462 r_scangle_it 4.717 r_scbond_it 2.859 r_mcangle_it 1.885 r_angle_refined_deg 1.681 r_angle_other_deg 1.072 r_mcbond_it 1.003 r_mcbond_other 0.263 r_chiral_restr 0.097 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1024 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 33
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling