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Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris-HCl pH 8.5, 0.1M MgCl2, 0.4M MgTartrate, 9mM n-Decyl-beta-D-thiomaltoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.08 69.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.85 α = 90 b = 75.85 β = 90 c = 87.55 γ = 120
Symmetry Space Group P 31 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 225 mm CCD mirrors 2006-10-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.9782, 0.9790, 0.96 MAX II I911-3
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 2.2 40 99.4 0.074 19 5.8 13359 13273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 98.9 0.561 4.05 5.8 3574
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.3 37.93 12615 658 99.36 0.19869 0.19647 0.1936 0.2408 0.2355 RANDOM 54.746
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_1_deg 19.764 r_dihedral_angle_3_deg 17.264 r_dihedral_angle_4_deg 15.888 r_scangle_it 4.576 r_scbond_it 2.96 r_mcangle_it 2.078 r_angle_refined_deg 1.994 r_mcbond_it 1.398 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.747 r_dihedral_angle_1_deg 19.764 r_dihedral_angle_3_deg 17.264 r_dihedral_angle_4_deg 15.888 r_scangle_it 4.576 r_scbond_it 2.96 r_mcangle_it 2.078 r_angle_refined_deg 1.994 r_mcbond_it 1.398 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.253 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1059 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction XSCALE data scaling autoSHARP phasing