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Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, A272
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOP
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 4.37 71.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.377 α = 90 b = 252.959 β = 90 c = 260.869 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 EIGER2 X 16M 2019-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
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 3 49.54 100 0.081 0.086 0.999 18.5 8.576 108427 84.753
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 3 3.08 100 1.125 1.198 0.802 2.2 8.529
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 6EOP 3 49.54 103005 5422 99.96 0.1987 0.1969 0.2003 0.2323 0.2311 RANDOM 101.429
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] 1.22 4.18 -5.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.108 r_dihedral_angle_4_deg 14.46 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 6.138 r_angle_refined_deg 1.152 r_angle_other_deg 0.853 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.108 r_dihedral_angle_4_deg 14.46 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 6.138 r_angle_refined_deg 1.152 r_angle_other_deg 0.853 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19949 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing