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Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocycle 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 6.5, 5% Tacsimate pH 7, 10% 1,4-Dioxane, 14% PEGGMME 5000
Crystal Properties Matthews coefficient Solvent content 4.11 70.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 263.254 α = 90 b = 263.254 β = 90 c = 91.234 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 9M 2018-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.978 NSLS-II 17-ID-1
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 3.569 84.704 99.88 0.1076 0.1521 0.985 6.85 4.7 43243 75.378971446
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 3.569 3.697 99.95 0.724
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 4LTE 3.56914708689 65.8135 1.34363886775 43228 2066 99.9098620196 0.164395090488 0.16203545477 0.1652 0.21090305456 0.214 71.2088458101
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 14.9625104584 f_angle_d 0.476083335956 f_chiral_restr 0.0378714219735 f_plane_restr 0.00312367984873 f_bond_d 0.00183835676499
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15596 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction autoPROC data scaling PHASER phasing