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Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, A241
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.46 M Na citrate
Crystal Properties Matthews coefficient Solvent content 4.36 71.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.034 α = 90 b = 252.779 β = 90 c = 261.235 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M-F 2019-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 44.07 100 0.087 0.093 0.999 18.9 8.418 132897 72.077
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 1.291 1.373 0.738 2.08 8.667
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6EOO 2.8 44.07 126252 6645 99.96 0.2143 0.2127 0.2126 0.2446 0.2419 RANDOM 74.385
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] 0.64 2.64 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_4_deg 13.918 r_dihedral_angle_1_deg 6.647 r_angle_refined_deg 1.187 r_angle_other_deg 1.056 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_4_deg 13.918 r_dihedral_angle_1_deg 6.647 r_angle_refined_deg 1.187 r_angle_other_deg 1.056 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20527 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing