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Crystal Structure of Human DPP4 Bound to TAK-986
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9M pdb entry 1R9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop, vapor diffusion 277 20% PEG MME 2000, 100 mM Bicine, pH 8-8.5, sitting drop, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.166 α = 90 b = 122.886 β = 114.59 c = 144.909 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 92 CCD ADSC QUANTUM 315r 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.75 50 98.9 0.087 9.6 3.2 101631 100525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 98.6 0.514 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1R9M 2.75 35 101701 95320 5026 98.65 0.20619 0.20338 0.2485 0.25961 0.2891 RANDOM 41.346
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] -1.08 0.04 0.97 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.267 r_dihedral_angle_3_deg 17.821 r_dihedral_angle_4_deg 17.155 r_dihedral_angle_1_deg 6.349 r_scangle_it 1.495 r_angle_refined_deg 1.222 r_scbond_it 0.925 r_angle_other_deg 0.875 r_mcangle_it 0.684 r_mcbond_it 0.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.267 r_dihedral_angle_3_deg 17.821 r_dihedral_angle_4_deg 17.155 r_dihedral_angle_1_deg 6.349 r_scangle_it 1.495 r_angle_refined_deg 1.222 r_scbond_it 0.925 r_angle_other_deg 0.875 r_mcangle_it 0.684 r_mcbond_it 0.397 r_symmetry_vdw_other 0.27 r_nbd_other 0.203 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.19 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_other 0.1 r_nbtor_other 0.095 r_chiral_restr 0.072 r_mcbond_other 0.061 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23879 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 372
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection