4M1C

Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IOFPDB ENTRY 4IOF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291.150.1M Sodium cacodylate, pH6.5, 0.2M MgCl2, 10% PEG-3000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.0439.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.583α = 90
b = 135.324β = 90
c = 368.524γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315r2013-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.549.196.60.1595.5355633556352.45
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.5696.70.685.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4IOF3.500749.0641.343453635509199796.250.23020.22780.27
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_d9.745
f_angle_d0.533
f_chiral_restr0.021
f_plane_restr0.003
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21507
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms2

Software

Software
Software NamePurpose
HKL-3000data collection
PHASESphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling