3IOL

Crystal structure of Glucagon-Like Peptide-1 in complex with the extracellular domain of the Glucagon-Like Peptide-1 Receptor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92910.1M 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 coefficientSolvent content
238.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.67α = 90
b = 42.67β = 90
c = 95.09γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.195980.111147105851034825.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2980.4495.371132

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 ligand2.128.538786835742997.850.180580.178160.22622RANDOM13.663
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.406
r_dihedral_angle_3_deg14.042
r_dihedral_angle_4_deg13.082
r_dihedral_angle_1_deg6.462
r_scangle_it4.717
r_scbond_it2.859
r_mcangle_it1.885
r_angle_refined_deg1.681
r_angle_other_deg1.072
r_mcbond_it1.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.406
r_dihedral_angle_3_deg14.042
r_dihedral_angle_4_deg13.082
r_dihedral_angle_1_deg6.462
r_scangle_it4.717
r_scbond_it2.859
r_mcangle_it1.885
r_angle_refined_deg1.681
r_angle_other_deg1.072
r_mcbond_it1.003
r_mcbond_other0.263
r_chiral_restr0.097
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1024
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms33

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling