4PHU

Crystal structure of Human GPR40 bound to allosteric agonist TAK-875


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EJ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE829429-31% Peg 400,100 mM Tris pH 8.0. 0.2 M Na Malonate,200 uM TAK-875
2LIPIDIC CUBIC PHASE7.229439.8 % Peg 400, 100 mM Bis-Tris-Propane pH 7.2, 0.1 Ammonium Phosphate (monobasic), 200 uM TAK-875

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101α = 90
b = 61.74β = 108.9
c = 105.7γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-05-22MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 300 mm CCD2012-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976ALS5.0.3
2SYNCHROTRONAPS BEAMLINE 23-ID-B1.0APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.3310098.20.120.1330.0568.352602226022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.46900.6230.6230.34913.43506

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4EJ42.3323025947131297.850.19990.19810.2331RANDOM48.541
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]
2.17-0.24-0.55-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.679
r_dihedral_angle_3_deg16.263
r_dihedral_angle_4_deg15.969
r_dihedral_angle_1_deg4.978
r_mcangle_it1.894
r_angle_refined_deg1.118
r_mcbond_it1.104
r_mcbond_other1.103
r_angle_other_deg0.743
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.679
r_dihedral_angle_3_deg16.263
r_dihedral_angle_4_deg15.969
r_dihedral_angle_1_deg4.978
r_mcangle_it1.894
r_angle_refined_deg1.118
r_mcbond_it1.104
r_mcbond_other1.103
r_angle_other_deg0.743
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3272
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms127

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building