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Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B142
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 Na citrate
Crystal Properties Matthews coefficient Solvent content 4.2 70.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.443 α = 90 b = 149.443 β = 90 c = 269.388 γ = 120
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 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 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 2.44 49.74 100 0.073 0.076 0.999 22.96 13.186 126021 67.347
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 2.44 2.5 100 1.255 1.309 0.748 2.06 12.204
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 2.44 49.74 119719 6301 99.98 0.2165 0.2146 0.2184 0.2531 0.2519 RANDOM 64.497
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 0.5 1 -3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.502 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 17.633 r_dihedral_angle_1_deg 8.274 r_angle_refined_deg 1.579 r_angle_other_deg 1.242 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.502 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 17.633 r_dihedral_angle_1_deg 8.274 r_angle_refined_deg 1.579 r_angle_other_deg 1.242 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13151 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 82
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing