TR-SMX closed state structure (0-5ms) of bacteriorhodopsin
Serial Crystallography (SX)
Serial Crystallography (SX)
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5B6Z | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIPIDIC CUBIC PHASE | 5.6 | 294 | 100 mM Na/K Phosphate buffer pH 5.6 30 % PEG 2000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.44 | 49.63 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 62 | α = 90 |
| b = 62 | β = 90 |
| c = 110.3 | γ = 120 |
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | PIXEL | DECTRIS EIGER X 16M | | 2018-07-22 | M | SINGLE WAVELENGTH |
| 2 | 1 | x-ray | 298 | PIXEL | DECTRIS EIGER X 16M | | 2018-07-22 | M | SINGLE WAVELENGTH |
| 3 | 1 | x-ray | 298 | PIXEL | DECTRIS EIGER X 16M | | 2018-07-22 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
| 2 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
| 3 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
| 2 | | injection |
| 3 | | injection |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | high viscosity injector | undefined (µl/min) | undefined (µm) | | glass capillary | | LCP |
| 2 | | undefined (µl/min) | undefined (µm) | | flass capillary | | LCP |
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 |
|---|
| 3 | 2.1 | 38.5 | 100 | 0.99 | 0.034 | 13.3 | 984.9 | | 13882 | | | |
| 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) |
|---|
| 3 | 2.1 | 2.18 | 100 | | 0.52 | 0.86 | 1.33 | 24.6 | |
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 | THROUGHOUT | 5B6Z | 2.6 | 38.47 | 0.02 | 6737 | 419 | 90.82 | 0.2529 | 0.2494 | 0.3012 | 83.73 |
| 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 | 9.8572 |
| f_angle_d | 0.447 |
| f_chiral_restr | 0.0347 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.0027 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1790 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 8 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
