3C59

Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1M 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 coefficientSolvent content
4.0869.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.85α = 90
b = 75.85β = 90
c = 87.55γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2006-10-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-30.9782, 0.9790, 0.96MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.24099.40.074195.81335913273
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.398.90.5614.055.83574

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.337.931261565899.360.198690.196470.2408RANDOM54.746
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.747
r_dihedral_angle_1_deg19.764
r_dihedral_angle_3_deg17.264
r_dihedral_angle_4_deg15.888
r_scangle_it4.576
r_scbond_it2.96
r_mcangle_it2.078
r_angle_refined_deg1.994
r_mcbond_it1.398
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.747
r_dihedral_angle_1_deg19.764
r_dihedral_angle_3_deg17.264
r_dihedral_angle_4_deg15.888
r_scangle_it4.576
r_scbond_it2.96
r_mcangle_it2.078
r_angle_refined_deg1.994
r_mcbond_it1.398
r_nbtor_refined0.307
r_symmetry_hbond_refined0.253
r_nbd_refined0.228
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.164
r_chiral_restr0.136
r_bond_refined_d0.019
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms1059
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing