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Crystal Structure of Insulin Degrading Enzyme in Complex with macrophage inflammatory protein 1 alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WBY PDB entry 2wby
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 13% PEGMME 5000, 100mM HEPES, pH 7.0, 10%, Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.68 66.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 262.737 α = 90 b = 262.737 β = 90 c = 90.502 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 CCD ADSC QUANTUM 315 bent conical Si-mirror (Rh coating) 2008-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9762 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3 50 99.64 0.142 0.142 5 67989 67744 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.11 100 0.53 0.514 3 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2wby 3 30 1 67989 67744 3612 99.6 0.185 0.183 0.1924 0.237 0.2402 RANDOM 50.95
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] 0.8 0.4 0.8 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.977 r_dihedral_angle_3_deg 21.561 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_1_deg 6.488 r_scangle_it 3.024 r_scbond_it 1.694 r_angle_refined_deg 1.588 r_mcangle_it 1.066 r_mcbond_it 0.523 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.977 r_dihedral_angle_3_deg 21.561 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_1_deg 6.488 r_scangle_it 3.024 r_scbond_it 1.694 r_angle_refined_deg 1.588 r_mcangle_it 1.066 r_mcbond_it 0.523 r_chiral_restr 0.107 r_bond_refined_d 0.014 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15766 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 38
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling