6DK5
The X-ray crystal structure of human endothelin-1, a polypeptide hormone regulator of blood pressure
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 310 | 4 uL 15 mg/mL aqueous endothelin + 6 uL reservoir solution (20-25% MPD, 0.2 M MES, pH 6.5) + 2 uL 0.2 M MES, pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.71 | 29.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.328 | α = 90 |
b = 27.328 | β = 90 |
c = 79.538 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | AREA DETECTOR | SDMS | 1997-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.85 | 80 | 99.6 | 0.257 | 0.257 | 0.283 | 0.086 | 0.947 | 4.6 | 7.7 | 2534 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 5GLH | 1.85 | 23.67 | 2534 | 143 | 92.92 | 0.2079 | 0.20387 | 0.28373 | RANDOM | 32.583 |
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] | |
0.01 | 0.01 | 0.01 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.176 |
r_dihedral_angle_3_deg | 20.16 |
r_dihedral_angle_1_deg | 8.03 |
r_long_range_B_refined | 7.759 |
r_long_range_B_other | 7.752 |
r_mcangle_it | 4.635 |
r_mcangle_other | 4.629 |
r_scangle_other | 3.994 |
r_mcbond_it | 3.171 |
r_mcbond_other | 3.144 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 334 |
Nucleic Acid Atoms | |
Solvent Atoms | 24 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SDMS | data reduction |
Aimless | data scaling |
PHASER | phasing |