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Crystal structure of DPP8 in complex with the EIL peptide (SLRFLFEGQRIADNH)
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 6.75 277 0.46 M Na citrate pH 6.75
Crystal Properties Matthews coefficient Solvent content 4.12 70.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.045 α = 90 b = 245.283 β = 90 c = 261.439 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 PILATUS 6M-F 2019-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99989 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 3 49.17 99.9 0.091 0.097 0.999 20.41 8.427 104482 77.091
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 3 3.08 100 1.271 1.351 0.71 1.99 8.527
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 3 49.17 99257 5225 99.95 0.193 0.1913 0.1931 0.2263 0.2225 RANDOM 91.044
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 4.85 -2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.676 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_1_deg 5.946 r_angle_refined_deg 1.133 r_angle_other_deg 0.849 r_chiral_restr 0.068 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 33.676 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_1_deg 5.946 r_angle_refined_deg 1.133 r_angle_other_deg 0.849 r_chiral_restr 0.068 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 20694 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 3
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing