6YVR
Crystal structure of the neurotensin receptor 1 in complex with the peptide full agonist NTS8-13
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4XEE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.4 | 277.1 | 50mM glycine 1M NaCl 8.3% (w/v) PEG4000 Cryoprotectant solution contained: 50mM glycine pH 9.4 1M NaCl 100nM NTS8-13 15% (v/v) PEG600 15% (v/v) glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.49 | 72.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.886 | α = 90 |
b = 114.001 | β = 90 |
c = 195.424 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS EIGER X 16M | 2017-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000031 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.458 | 29.633 | 93.9 | 0.094 | 0.098 | 0.028 | 0.999 | 15.2 | 12 | 59974 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.458 | 2.647 | 1.711 | 1.801 | 0.555 | 0.597 | 1.6 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4XEE | 2.458 | 29.633 | 59974 | 2958 | 81.168 | 0.229 | 0.2284 | 0.2375 | 70.765 |
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] | |
-0.652 | -0.561 | 1.213 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.931 |
r_dihedral_angle_4_deg | 21.694 |
r_dihedral_angle_3_deg | 14.168 |
r_lrange_it | 7.736 |
r_lrange_other | 7.736 |
r_scangle_it | 6.42 |
r_scangle_other | 6.42 |
r_dihedral_angle_1_deg | 5.345 |
r_mcangle_it | 5.025 |
r_mcangle_other | 5.025 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7134 |
Nucleic Acid Atoms | |
Solvent Atoms | 48 |
Heterogen Atoms | 168 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |