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Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B114
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 mM Na citrate
Crystal Properties Matthews coefficient Solvent content 4.2 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.505 α = 90 b = 149.505 β = 90 c = 269.331 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 EIGER2 X 16M 2020-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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 2.45 48.94 100 0.069 0.072 1 23.16 13.161 124546 69.989
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 2.45 2.51 100 1.468 1.532 0.764 2.02 12.27
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 2.45 48.94 118318 6228 99.98 0.1944 0.1926 0.1975 0.2278 0.2305 RANDOM 65.657
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] 0.92 0.46 0.92 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.618 r_dihedral_angle_4_deg 20.409 r_dihedral_angle_3_deg 16.295 r_dihedral_angle_1_deg 7.68 r_angle_refined_deg 1.582 r_angle_other_deg 1.311 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.618 r_dihedral_angle_4_deg 20.409 r_dihedral_angle_3_deg 16.295 r_dihedral_angle_1_deg 7.68 r_angle_refined_deg 1.582 r_angle_other_deg 1.311 r_chiral_restr 0.07 r_bond_refined_d 0.009 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 13139 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 96
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing