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Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Glucagon and Substrate-selective Macrocyclic Inhibitor 63
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M HEPES pH 7.0, 12% Tacsimate pH 7.0, 13% PEGMME, 10% Dioxane
Crystal Properties Matthews coefficient Solvent content 4.01 69.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 263.119 α = 90 b = 263.119 β = 90 c = 90.322 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 EIGER X 16M 2018-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979341 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3.18 131.559 100 0.369 0.378 0.083 0.991 10.98 20.9 60302 57.9001204686
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.181 3.2356
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4LTE 3.18071730876 131.559 1.33583552402 60257 2869 99.9270327192 0.178934820394 0.176784619198 0.1784 0.222083555612 0.2242 R-free arrays for test set were copied from a different, previously refined crystal structure of ligand-bound IDE (different crystal, but identical protein and ligands). Additionally, Rfree array for test set was further expanded to resolution range of crystal. 51.5855318537
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 14.233969918 f_angle_d 0.645294260527 f_chiral_restr 0.0416953974471 f_plane_restr 0.00416801638865 f_bond_d 0.00382731870951
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15800 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction autoPROC data scaling PHASER phasing