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Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Substrate-selective Macrocyclic Inhibitor 37
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 6.8 298 0.1 M HEPES, 12% Tacsimate, 20% PEGMME-5000, 10% 1,4-dioxane
Crystal Properties Matthews coefficient Solvent content 4.13 70.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 264.486 α = 90 b = 264.486 β = 90 c = 91.094 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 CCD ADSC QUANTUM 315 2015-10-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.116 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.956 48.48 99.8 16.34 12.4 148881 63.5189271246
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 2.956 3.062 98.88 1.91
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 2.95624845742 48.4799486587 1.35094572484 148838 1997 99.8008515774 0.162016770659 0.160914089223 0.1632 0.202629282797 0.2047 60.7670774468
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 16.4771571885 f_angle_d 0.842663703044 f_chiral_restr 0.0514632526269 f_bond_d 0.00597916292666 f_plane_restr 0.00513063052414
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15653 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing