1W1I

Crystal structure of dipeptidyl peptidase IV (DPPIV or CD26) in complex with adenosine deaminase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N1MPDB ENTRIES 1N1M AND 1KRM
experimental modelPDB 1KRMPDB ENTRIES 1N1M AND 1KRM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8.00
Crystal Properties
Matthews coefficientSolvent content
3.160.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.065α = 90
b = 168.504β = 100.54
c = 236.842γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
13.033085.30.09102.31008171
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)
13.033.1581.30.42.12.3

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 REPLACEMENTTHROUGHOUTPDB ENTRIES 1N1M AND 1KRM3.033098926204885.50.2240.2240.257RANDOM52.46
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]
4.451.75-2.35-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.827
r_dihedral_angle_3_deg19.946
r_dihedral_angle_4_deg19.79
r_dihedral_angle_1_deg5.963
r_angle_refined_deg1.34
r_mcangle_it1.141
r_scangle_it1.053
r_mcbond_it0.646
r_scbond_it0.608
r_symmetry_hbond_refined0.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.827
r_dihedral_angle_3_deg19.946
r_dihedral_angle_4_deg19.79
r_dihedral_angle_1_deg5.963
r_angle_refined_deg1.34
r_mcangle_it1.141
r_scangle_it1.053
r_mcbond_it0.646
r_scbond_it0.608
r_symmetry_hbond_refined0.282
r_symmetry_vdw_refined0.275
r_nbd_refined0.232
r_xyhbond_nbd_refined0.187
r_chiral_restr0.116
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_refined
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms35087
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms790

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing