RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.08 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6DHE | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 298 | 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.18 | 56.2 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 116.92 | α = 90 |
| b = 221.635 | β = 90 |
| c = 307.834 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 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 | 298 | CCD | RAYONIX MX340-HS | | 2018-11-27 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.30183 | SLAC LCLS | MFX |
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 | 2.08 | 33.64 | 99.77 | 0.98 | 13.2 | 89.1 | | 474828 | | | 34.44 |
| 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 | 2.08 | 2.12 | | | 0.054 | | | |
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 | 6DHE | 2.08 | 33.64 | 1.33 | 473865 | 4204 | 99.6 | 0.1819 | 0.1814 | 0.18 | 0.2403 | 0.24 | 41.28 |
| 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 | 21.5532 |
| f_angle_d | 1.5361 |
| f_chiral_restr | 0.063 |
| f_bond_d | 0.0149 |
| f_plane_restr | 0.0095 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 47681 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2029 |
| Heterogen Atoms | 2510 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| cctbx.xfel | data reduction |
| PHASER | phasing |
