4GS8

Structure analysis of cysteine free insulin degrading enzyme (ide) with compound bdm43079 [{[(s)-2-(1h-imidazol-4-yl)-1-methylcarbamoyl-ethylcarbamoyl]-methyl}-(3-phenyl-propyl)-amino]-acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CWW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP710-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
Crystal Properties
Matthews coefficientSolvent content
3.9969.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 263.553α = 90
b = 263.553β = 90
c = 91.095γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2010-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.9950100694692
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9950100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CWW2.995016946969469367999.80.1810.1780.235RANDOM40.11
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]
1.090.551.09-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.971
r_dihedral_angle_4_deg22.179
r_dihedral_angle_3_deg21.717
r_dihedral_angle_1_deg6.445
r_scangle_it4.17
r_scbond_it2.355
r_angle_refined_deg1.818
r_mcangle_it1.415
r_mcbond_it0.681
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.971
r_dihedral_angle_4_deg22.179
r_dihedral_angle_3_deg21.717
r_dihedral_angle_1_deg6.445
r_scangle_it4.17
r_scbond_it2.355
r_angle_refined_deg1.818
r_mcangle_it1.415
r_mcbond_it0.681
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms15590
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms60

Software

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