6EDS

Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with Glucagon and Substrate-selective Macrocyclic Inhibitor 63


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LTE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1M HEPES pH 7.0, 12% Tacsimate pH 7.0, 13% PEGMME, 10% Dioxane
Crystal Properties
Matthews coefficientSolvent content
4.0169.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 263.119α = 90
b = 263.119β = 90
c = 90.322γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.979341NSLS-II17-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.18131.5591000.3690.3780.0830.99110.9820.96030257.9001204686
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.1813.2356

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4LTE3.18071730876131.5591.3358355240260257286999.92703271920.1789348203940.1767846191980.222083555612R-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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.233969918
f_angle_d0.645294260527
f_chiral_restr0.0416953974471
f_plane_restr0.00416801638865
f_bond_d0.00382731870951
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15800
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms126

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
autoPROCdata scaling
PHASERphasing