6YXG
Cryogenic human adiponectin receptor 2 (ADIPOR2) with Tb-XO4 ligand determined by Serial Crystallography (SSX) using CrystalDirect
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LWY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 293 | 30 or 50 nL bolus overlaid with 600 nL precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0. 30-150 nL of Tb-XO4 soaking solution with a final conc. of 5 - 25 mM was delivered onto LCP crystallisation drop. Crystallisation experiments were carried out at the HTX facility of EMBL Grenoble. LCP bolus were harvested automatically at cryogenic condition using CrystalDirect technology. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.55 | 65.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.61 | α = 90 |
b = 100.69 | β = 90 |
c = 110.51 | γ = 90 |
Symmetry | |
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Space Group | P 21 2 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 | 2019-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.72 | SLS | X06SA |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | fixed target |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 3 | 50 | 100 | 0.99 | 7.33 | 34.82 | 32012 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3 | 3.1 | 100 | 0.3 | 1.48 |
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 | 5LWY | 3.01 | 48 | 17076 | 971 | 99.9 | 0.2148 | 0.2125 | 0.2515 | RANDOM | 81.27 |
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] | |
17.3193 | 30.4449 | -47.7642 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 21.61 |
t_omega_torsion | 3.32 |
t_angle_deg | 1.1 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4073 |
Nucleic Acid Atoms | |
Solvent Atoms | 19 |
Heterogen Atoms | 302 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |