4GSF

The structure analysis of cysteine free insulin degrading enzyme (ide) with (s)-2-{2-[carboxymethyl-(3-phenyl-propionyl)-amino]-acetylamino}-3-(3h-imidazol-4-yl)-propionic acid methyl ester


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 287K
Crystal Properties
Matthews coefficientSolvent content
3.9568.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 263.179α = 90
b = 263.179β = 90
c = 90.557γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-02-12MSINGLE 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
12.75010098494935812
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.750100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CWW2.750984949358149131000.2260.1760.1740.22RANDOM38.45
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]
0.760.380.76-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.872
r_dihedral_angle_4_deg19.338
r_dihedral_angle_3_deg18.559
r_dihedral_angle_1_deg6.651
r_scangle_it5.848
r_scbond_it3.411
r_angle_refined_deg2.008
r_mcangle_it1.918
r_mcbond_it0.925
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.872
r_dihedral_angle_4_deg19.338
r_dihedral_angle_3_deg18.559
r_dihedral_angle_1_deg6.651
r_scangle_it5.848
r_scbond_it3.411
r_angle_refined_deg2.008
r_mcangle_it1.918
r_mcbond_it0.925
r_chiral_restr0.127
r_bond_refined_d0.023
r_gen_planes_refined0.009
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 Atoms15526
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms62

Software

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