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Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G47 PDB entry 2G47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 20% PEG3350, 0.2 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.754 α = 90 b = 116.087 β = 98.09 c = 123.923 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2011-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 122.69 98.8 0.07 7.9 3.7 119894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 0.606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2G47 2.21 122.69 107879 1008 98.63 0.20926 0.20884 0.2077 0.25606 0.2579 RANDOM 46.756
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] 3.22 0.73 -0.82 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.123 r_dihedral_angle_4_deg 18.05 r_dihedral_angle_3_deg 15.826 r_dihedral_angle_1_deg 5.269 r_angle_refined_deg 1.331 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.123 r_dihedral_angle_4_deg 18.05 r_dihedral_angle_3_deg 15.826 r_dihedral_angle_1_deg 5.269 r_angle_refined_deg 1.331 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15660 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction PHASER phasing