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Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, 91
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 273 0.46 M Na citrate
Crystal Properties Matthews coefficient Solvent content 4.45 72.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.598 α = 90 b = 153.598 β = 90 c = 270.222 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 2020-02-12 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 2.8 49.43 100 0.091 0.095 0.999 19.17 13.177 88413 78.124
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 2.8 2.87 100 1.546 1.606 0.792 2.04 13.645
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 2.8 49.43 83992 4421 99.97 0.2107 0.209 0.2123 0.2423 0.2408 RANDOM 89.573
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] 2.07 1.03 2.07 -6.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_3_deg 14.126 r_dihedral_angle_4_deg 13.966 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.365 r_angle_other_deg 0.866 r_chiral_restr 0.072 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 34.629 r_dihedral_angle_3_deg 14.126 r_dihedral_angle_4_deg 13.966 r_dihedral_angle_1_deg 6.085 r_angle_refined_deg 1.365 r_angle_other_deg 0.866 r_chiral_restr 0.072 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 13435 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 206
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing