Light structure of sensory rhodopsin-II solved by serial millisecond crystallography 120-150 milliseconds time-bin
X-RAY DIFFRACTION
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1H68 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | LIPIDIC CUBIC PHASE | 296 | CaCl2 150mM, Glycine 100mM, 38%(v/v) PEG 400, pH 7.5 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.83 | 56.47 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 89.75 | α = 90 |
| b = 131.7 | β = 90 |
| c = 51 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | DECTRIS EIGER X 16M | 2019-05-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0000342 | SLS | X06SA |
Serial Crystallography
| Sample delivery method | ||
|---|---|---|
| Diffraction ID | Description | Sample Delivery Method |
| 1 | injection | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.95 | 44.88 | 100 | 0.973 | 5.11 | 82.74 | 4429 | 35.98 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.34 | 44.9 | 0.975 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.95 | 44.88 | 1.35 | 4429 | 787 | 67.34 | 0.2489 | 0.2475 | 0.2475 | 0.2733 | 0.2735 | 45.16 | |||||
| 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 | 16.5642 |
| f_angle_d | 1.6506 |
| f_chiral_restr | 0.0722 |
| f_bond_d | 0.0124 |
| f_plane_restr | 0.0124 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1580 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 21 |
| Heterogen Atoms | 21 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHASER | phasing |














