4FFW

Crystal Structure of Dipeptidyl Peptidase IV (DPP4, DPP-IV, CD26) in Complex with Fab + sitagliptin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.92892.2-2.7 M ammonium sulfate, 0.1 M Tris 7.5-7.9, vapor diffusion, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.6866.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.77α = 90
b = 200.86β = 93.64
c = 97.93γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3153X3 CCD ARRAY2010-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
12.9100.4399.20.0810.83.78263482634
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.0699.20.4220.4221.73.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.929.9978420412399.090.287770.286540.31094RANDOM93.533
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]
-0.05-0.010.1-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.295
r_dihedral_angle_3_deg13.698
r_dihedral_angle_4_deg11.052
r_dihedral_angle_1_deg4.556
r_scangle_it3.017
r_scbond_it1.762
r_mcangle_it1.35
r_angle_refined_deg0.797
r_mcbond_it0.705
r_angle_other_deg0.648
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.295
r_dihedral_angle_3_deg13.698
r_dihedral_angle_4_deg11.052
r_dihedral_angle_1_deg4.556
r_scangle_it3.017
r_scbond_it1.762
r_mcangle_it1.35
r_angle_refined_deg0.797
r_mcbond_it0.705
r_angle_other_deg0.648
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms18171
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms56

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction