Structure of Chloride ion pumping rhodopsin (ClR) with NTQ motif 100 ps after light activation (2.63mJ/mm2)
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5G28 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIPIDIC CUBIC PHASE | 7 | 293 | monoolein mixture in syringe |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.85 | 56.85 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 103.37 | α = 90 |
| b = 50.09 | β = 109.69 |
| c = 69.39 | γ = 90 |
| Symmetry |
|---|
| Space Group | C 1 2 1 |
|---|
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 | | 2018-10-23 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.3 | SLAC LCLS | CXI |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | injection |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 100 (fs) | | | 9.54 (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | 22474 | | |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | LCP injector | undefined (µl/min) | undefined (µm) | | | | |
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 | 1.77 | 20.9 | 100 | 0.9786 | 5.17 | 268 | | 33081 | | | 5.5 |
| 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 | 1.77 | 1.8 | 100 | | 0.6918 | 1.54 | 63.2 | |
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 | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5g28 | 1.85 | 20.64 | 27269 | 1373 | 94.96 | 0.2611 | 0.2586 | 0.3076 | 10.45 |
| 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 | 18.7409 |
| f_angle_d | 1.2511 |
| f_chiral_restr | 0.0727 |
| f_bond_d | 0.008 |
| f_plane_restr | 0.0073 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2072 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 106 |
| Heterogen Atoms | 121 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| Coot | model building |
| PHENIX | phasing |
