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Crystal structure of DPP8 in complex with a b-lactam based inhibitor, A296.1
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 4.3 71.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.264 α = 90 b = 250.38 β = 90 c = 261.202 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 2019-11-19 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 2.65 49.05 100 0.061 0.065 0.999 21.75 8.536 154339 73.19
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 2.65 2.72 100 1.002 1.064 0.791 2.19 8.732
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 2.65 49.05 146621 7717 99.97 0.2186 0.2172 0.2192 0.2444 0.2435 RANDOM 76.41
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] -0.59 3.82 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.961 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 12.637 r_dihedral_angle_1_deg 5.66 r_angle_refined_deg 1.175 r_angle_other_deg 0.825 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.961 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 12.637 r_dihedral_angle_1_deg 5.66 r_angle_refined_deg 1.175 r_angle_other_deg 0.825 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19980 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 104
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing