3N56
Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 13% PEGMME-5000, 10% TACSIMATE, 10% DIOXANE, 100 mM Na-HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.86 | 68.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 264.036 | α = 90 |
b = 264.036 | β = 90 |
c = 90.645 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | MIRRORS | 2009-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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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 | 3.102 | 50 | 96.54 | 0.20299 | 0.078 | 10.3 | 2.5 | 63372 | 62152 | 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) | ||||||||||
3.102 | 3.182 | 98.64 | 0.295 | 0.462 | 1.8 | 2.5 | 4642 |
Refinement
Statistics | |||||||||||||||||||
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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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3cww | 3.102 | 50 | 63359 | 62152 | 1206 | 96.54 | 0.203 | 0.20221 | 0.243 | RANDOM | 54.03 |
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] | |
1.26 | 0.63 | 1.26 | -1.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.363 |
r_dihedral_angle_3_deg | 18.821 |
r_dihedral_angle_4_deg | 18.483 |
r_dihedral_angle_1_deg | 5.375 |
r_scangle_it | 1.356 |
r_angle_refined_deg | 1.166 |
r_mcangle_it | 0.728 |
r_scbond_it | 0.725 |
r_mcbond_it | 0.381 |
r_chiral_restr | 0.083 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15572 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |