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Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The crystal is grown in a condition containing PEG 2K MME buffered by Tris pH 7
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.35 α = 65.25 b = 106.176 β = 70.43 c = 121.127 γ = 75.86
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 EIGER X 16M 2022-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.807 106.9 64.6 0.048 0.048 5.4 2.3 220955
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.807 1.955 15.4 0.459 0.459 1.6 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6EOR 1.81 106.09 219248 1707 64.56 0.1754 0.1752 0.2031 0.2271 RANDOM 34.669
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] -0.06 0.07 -0.02 -0.04 -0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.955 r_dihedral_angle_4_deg 19.179 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 7.188 r_angle_refined_deg 1.357 r_angle_other_deg 1.191 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.955 r_dihedral_angle_4_deg 19.179 r_dihedral_angle_3_deg 12.978 r_dihedral_angle_1_deg 7.188 r_angle_refined_deg 1.357 r_angle_other_deg 1.191 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27210 Nucleic Acid Atoms Solvent Atoms 1653 Heterogen Atoms 281
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction X-GEN data reduction autoPROC data scaling PHASER phasing