4N6H
1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4EJ4 | PDB ENTRY 4EJ4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LCP | 293 | 31-34% (v/v) PEG 400, 0.095 to 0.12 M K/Na tartrate, 5% (v/v) ethylene glycol, 100 mM MES buffer at pH 6.1-6.2, LCP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.37 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.23 | ¦Á = 90 |
b = 72.851 | ¦Â = 107.48 |
c = 84.408 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | MARMOSAIC 300 mm CCD | mirrors | 2013-04-20 | M | SINGLE WAVELENGTH | |||||
2 | 1 | CCD | MARMOSAIC 300 mm CCD | mirrors | 2013-06-16 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0330 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.8 | 40 | 98.5 | 0.104 | 16.4 | 4.5 | 45488 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.86 | 98.5 | 0.822 | 2.3 | 4.3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4EJ4 | 1.8 | 29.7 | 43157 | 2303 | 98.26 | 0.17271 | 0.17175 | 0.19028 | RANDOM | 39.313 |
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] | |
2.4 | 0.03 | -0.41 | -1.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.636 |
r_dihedral_angle_4_deg | 16.747 |
r_dihedral_angle_3_deg | 12.935 |
r_dihedral_angle_1_deg | 4.852 |
r_angle_refined_deg | 1.419 |
r_angle_other_deg | 0.851 |
r_chiral_restr | 0.085 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3089 |
Nucleic Acid Atoms | |
Solvent Atoms | 101 |
Heterogen Atoms | 341 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |