7ZBE
Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1U19 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 9 | 294 | 36 % PEG 600, 100 mM Bicine pH 9.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.51 | α = 90 |
b = 91.01 | β = 90 |
c = 151.11 | γ = 90 |
Symmetry | |
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Space Group | P 2 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 | 294 | PIXEL | PSI JUNGFRAU 1M | 2020-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SwissFEL ARAMIS BEAMLINE ESA | 1.38 | SwissFEL ARAMIS | ESA |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | injection |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.8 | 16.1 | 100 | 0.9926 | 0.0821 | 7.62 | 830.6 | 79305 | 30.05 |
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 | 1.8 | 1.86 | 100 | 0.9926 | 1.0906 | 0.95 | 556.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1U19 | 1.8 | 16.1 | 1.33 | 79098 | 1144 | 99.81 | 0.215 | 0.2146 | 0.2474 | 33.69 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.2025 |
f_angle_d | 0.9125 |
f_chiral_restr | 0.056 |
f_bond_d | 0.0085 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4801 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 352 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |