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Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 20% PEG 3350, 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 3.27 62.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.34 α = 90 b = 75.617 β = 110.199 c = 121.679 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 190 PIXEL DECTRIS EIGER X 16M silicon crystal (111) monochromator 2021-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97894 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.575 29.48 98.98 0.999 2 6.5 26023 63.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.57547 3.6 0.717
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1wcy 3.58 29.48 1.36 26023 1999 98.98 0.2289 0.2232 0.2245 0.2989 0.2954 77.02
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.0008 f_angle_d 0.6758 f_chiral_restr 0.0583 f_plane_restr 0.0053 f_bond_d 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11967 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 260
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing