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Crystal structure of human insulin-degrading enzyme in complex with insulin
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 7 10-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE
Crystal Properties Matthews coefficient Solvent content 3.8 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 262.319 α = 90 b = 262.319 β = 90 c = 90.609 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD 2007-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 99.9 0.13 21 7 109017 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 100 0.52 4.8 6.5
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 2.6 32.08 103440 5438 99.9 0.167 0.164 0.1682 0.218 0.2204 RANDOM 28.81
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.324 r_dihedral_angle_4_deg 22.892 r_dihedral_angle_3_deg 20.115 r_dihedral_angle_1_deg 6.809 r_scangle_it 5.42 r_scbond_it 3.421 r_angle_refined_deg 2.101 r_mcangle_it 1.881 r_mcbond_it 1.115 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.324 r_dihedral_angle_4_deg 22.892 r_dihedral_angle_3_deg 20.115 r_dihedral_angle_1_deg 6.809 r_scangle_it 5.42 r_scbond_it 3.421 r_angle_refined_deg 2.101 r_mcangle_it 1.881 r_mcbond_it 1.115 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.24 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.139 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 16202 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing