7P2L
thermostabilised 7TM domain of human mGlu5 receptor bound to photoswitchable ligand alloswitch-1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4OO9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 295 | 0.15-0.25 M ammonium phosphate dibasic, 22-24 % polyethylene glycol 400, either with 0.10 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.7-6.8 or 0.1 M HEPES pH 6.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 141.69 | α = 90 |
b = 43.4 | β = 99.38 |
c = 82.12 | γ = 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 | PIXEL | DECTRIS EIGER X 16M | 2020-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.54 | 49.11 | 100 | 0.253 | 0.997 | 6.35 | 10.66 | 16595 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.54 | 2.61 | 99 | 2.685 | 0.51 | 9.3 |
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 | 4oo9 | 2.54 | 49.11 | 15764 | 830 | 99.98 | 0.2298 | 0.2267 | 0.2853 | RANDOM | 69.807 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-3.72 | -2.45 | 8.63 | -3.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.438 |
r_dihedral_angle_3_deg | 15.733 |
r_dihedral_angle_4_deg | 14.162 |
r_dihedral_angle_1_deg | 5.936 |
r_angle_refined_deg | 1.306 |
r_angle_other_deg | 1.115 |
r_chiral_restr | 0.053 |
r_bond_refined_d | 0.004 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3238 |
Nucleic Acid Atoms | |
Solvent Atoms | 7 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |