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Crystal structure of dipeptidyl peptidase IV in complex with TAK-322
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 22% PEG MME 2000, 0.06M NP_Bicine_Na, 0.04M Bicine, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.84 56.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.686 α = 90 b = 122.398 β = 114.72 c = 144.01 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 100 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0000 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 35 182012
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.25 35 168006 8857 97.04 0.20855 0.20675 0.2037 0.24245 0.2406 RANDOM 52.676
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] -1.98 0.23 2.55 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.639 r_dihedral_angle_4_deg 18 r_dihedral_angle_3_deg 16.974 r_dihedral_angle_1_deg 6.339 r_scangle_it 1.678 r_angle_refined_deg 1.284 r_scbond_it 1.089 r_mcangle_it 0.742 r_mcbond_it 0.435 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.639 r_dihedral_angle_4_deg 18 r_dihedral_angle_3_deg 16.974 r_dihedral_angle_1_deg 6.339 r_scangle_it 1.678 r_angle_refined_deg 1.284 r_scbond_it 1.089 r_mcangle_it 0.742 r_mcbond_it 0.435 r_nbtor_refined 0.311 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23873 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 562
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling