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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 10-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K
Crystal Properties Matthews coefficient Solvent content 3.95 68.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 263.179 α = 90 b = 263.179 β = 90 c = 90.557 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 100 IMAGE PLATE MAR scanner 345 mm plate 2009-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 50 100 98494 93581 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 50 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3CWW 2.7 50 98494 93581 4913 100 0.226 0.176 0.174 0.1721 0.22 0.2184 RANDOM 38.45
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] 0.76 0.38 0.76 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.872 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 18.559 r_dihedral_angle_1_deg 6.651 r_scangle_it 5.848 r_scbond_it 3.411 r_angle_refined_deg 2.008 r_mcangle_it 1.918 r_mcbond_it 0.925 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.872 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 18.559 r_dihedral_angle_1_deg 6.651 r_scangle_it 5.848 r_scbond_it 3.411 r_angle_refined_deg 2.008 r_mcangle_it 1.918 r_mcbond_it 0.925 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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 Atoms Number Protein Atoms 15526 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 62
Software Software Software Name Purpose HKL-3000 data collection PHASES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling