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Crystal structure of DPP9 in complex with N-phosphono-(S)-3-aminopiperidine-2-one-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 18.0% w/v PEG 2K MME; 0.1 M Tris pH 7.25
Crystal Properties Matthews coefficient Solvent content 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.306 α = 65.24 b = 106.746 β = 71.02 c = 121.482 γ = 76.71
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2024-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.49 106.55 98.7 0.99 5.5 3.7 95210
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.74 0.68
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.49 106.55 95210 2036 72.31 0.17138 0.17036 0.21881 0.2096 RANDOM 47.351
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] -0.2 -0.01 0.11 0.3 -0.22 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.068 r_dihedral_angle_2_deg 8.137 r_long_range_B_refined 8.033 r_long_range_B_other 8.033 r_dihedral_angle_1_deg 7.223 r_mcangle_it 5.63 r_mcangle_other 5.63 r_scangle_other 5.504 r_mcbond_it 3.46 r_mcbond_other 3.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.068 r_dihedral_angle_2_deg 8.137 r_long_range_B_refined 8.033 r_long_range_B_other 8.033 r_dihedral_angle_1_deg 7.223 r_mcangle_it 5.63 r_mcangle_other 5.63 r_scangle_other 5.504 r_mcbond_it 3.46 r_mcbond_other 3.459 r_scbond_it 3.328 r_scbond_other 3.328 r_angle_refined_deg 1.375 r_angle_other_deg 0.536 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26205 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 218
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PHASER phasing