Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5J7A | |
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 |
|---|
| 2.32 | 47.04 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 62.32 | α = 90 |
| b = 62.32 | β = 90 |
| c = 111.1 | 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 | CS-PAD CXI-1 | | 2017-06-30 | 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 |
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 | 1.5 | 19.355 | 100 | 0.999 | 0.027 | 19 | 2005.6 | | 39064 | | | |
| 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 | 1.5 | 1.55 | 100 | | 0.084 | 0.63 | 2.3 | 122.6 | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5J7A | 1.5 | 19.355 | 1.35 | 38966 | 2363 | 99.84 | 0.1167 | 0.1151 | 0.12 | 0.1428 | 0.14 | |
| 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 | 14.231 |
| f_angle_d | 1.403 |
| f_chiral_restr | 0.26 |
| f_bond_d | 0.017 |
| f_plane_restr | 0.012 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1770 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 57 |
| Heterogen Atoms | 193 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHASER | phasing |
