3C5T

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C59PDB entry 3C59 without the ligand present

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
4.1270.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.91α = 90
b = 75.91β = 90
c = 87.77γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2006-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.00MAX 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
12.14098.30.06127.110.91757217273
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)
12.12.297.80.3957.311.12205

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3C59 without the ligand present2.136.5166071632190998.280.205030.203280.23809RANDOM40.26
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]
1.070.541.07-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.393
r_dihedral_angle_3_deg14.016
r_dihedral_angle_4_deg13.422
r_dihedral_angle_1_deg7.747
r_scangle_it4.385
r_scbond_it2.737
r_mcangle_it2.298
r_angle_refined_deg1.702
r_mcbond_it1.359
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.393
r_dihedral_angle_3_deg14.016
r_dihedral_angle_4_deg13.422
r_dihedral_angle_1_deg7.747
r_scangle_it4.385
r_scbond_it2.737
r_mcangle_it2.298
r_angle_refined_deg1.702
r_mcbond_it1.359
r_nbtor_refined0.313
r_nbd_refined0.23
r_symmetry_hbond_refined0.17
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_refined0.147
r_chiral_restr0.112
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 Atoms1055
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing