3NOX

Crystal structure of human DPP-IV in complex with Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BJMPDB entry 3BJM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298CRYSTALS GROWN FROM 2 UL EQUIVOLUME MIXTURE OF PROTEIN SOLUTION (0.1 M NACL, 20 MM TRIS-HCL BUFFER PH 7.8, 9.8 MG/ML PROTEIN) AND CRYSTALLIZATION SOLUTION (17% W/V PEG 3350, 15% W/V GLYCEROL, 200 MM MGCL2, 100 MM TRIS-HCL BUFFER PH 8.5). SUFFICIENT 100 MM LIGAND STOCK SOLUTION (NEAT DMSO) ADDED TO ACHIEVE 1 MM LIGAND CONCENTRATION. SOAKED OVERNIGHT. HARVESTED DIRECTLY AND CRYO-PRESERVED IN LN2., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.451α = 90
b = 67.072β = 90
c = 420.443γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q3152006-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.355086.50.113146.868839
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4350.92.63.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 3BJM2.33835.6241.4468723154086.110.19770.19610.264
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]
-4.828216.0882-11.26
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.594
f_angle_d1.158
f_chiral_restr0.078
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11875
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms258

Software

Software
Software NamePurpose
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling