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Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, L84
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 4.2 70.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.422 α = 90 b = 149.422 β = 90 c = 269.767 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 2019-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999890 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 2.6 43.74 100 0.111 0.116 0.999 16.2 12.647 104327 69.122
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 2.6 2.67 100 1.652 1.72 0.749 1.95 12.878
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 2.6 43.74 99110 5217 99.97 0.2242 0.2224 0.225 0.2596 0.2632 RANDOM 69.816
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] 0.89 0.45 0.89 -2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.556 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_3_deg 13.78 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 1.146 r_angle_other_deg 0.856 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.556 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_3_deg 13.78 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 1.146 r_angle_other_deg 0.856 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13054 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 72
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing