6PS6
XFEL beta2 AR structure by ligand exchange from Timolol to Timolol.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3D4S |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 293 | 0.1 M HEPES pH 7.0, 0.1 M Ammonium Sulfate, 30% PEG 400, 2 mM of target ligand Timolol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.48 | α = 90 |
b = 76.19 | β = 90 |
c = 171.96 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | PIXEL | CS-PAD CXI-1 | 2014-11-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.33 | SLAC LCLS | CXI |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | injection |
Injection | |||||||
---|---|---|---|---|---|---|---|
Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
1 | 0.2 |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 42 | 120 | 1.5 | 9.5 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 17952 | 80792 | 918091 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | 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 | 2.7 | 31.4 | 100 | 0.986 | 0.177 | 4.2 | 170.9 | 15738 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.7 | 2.89 | 0.246 | 1.855 |
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 | 3d4s | 2.7 | 31.35 | 15665 | 785 | 99.8 | 0.218 | 0.218 | 0.232 | RANDOM | 87.5 |
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] | |
-11.9832 | 5.8043 | 6.1788 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 2.95 |
t_omega_torsion | 2.01 |
t_angle_deg | 0.96 |
t_bond_d | 0.009 |
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 | 3478 |
Nucleic Acid Atoms | |
Solvent Atoms | 10 |
Heterogen Atoms | 226 |
Software
Software | |
---|---|
Software Name | Purpose |
PHASER | phasing |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
CrystFEL | data scaling |