3N57

Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human atrial natriuretic peptide (ANP)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729113% PEGMME-5000, 10% TACSIMATE, 10% DIOXANE, 100 mM Na-HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.968.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 264.101α = 90
b = 264.101β = 90
c = 91.186γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
13.0265092.630.206930.14420.75.4658892
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.0263.10493.20.2630.5623.75.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT3.0329.96154296.50.206930.20610.24154RANDOM40.259
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]
0.060.030.06-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.373
r_dihedral_angle_4_deg23.524
r_dihedral_angle_3_deg21.674
r_dihedral_angle_1_deg5.684
r_scangle_it1.798
r_angle_refined_deg1.279
r_scbond_it0.992
r_mcangle_it0.715
r_mcbond_it0.365
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.373
r_dihedral_angle_4_deg23.524
r_dihedral_angle_3_deg21.674
r_dihedral_angle_1_deg5.684
r_scangle_it1.798
r_angle_refined_deg1.279
r_scbond_it0.992
r_mcangle_it0.715
r_mcbond_it0.365
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15652
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling