5KAF
RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 7.5 | 293 | Crystal growth was as described in Kern et al. 2005, Biochim. Biophys. Acta-Bioenergetics and Ibrahim et al. 2015, Struct. Dyn. 2 (4), 041705, substituting C12E8 for beta-DM and Betaine for glycerol. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.69 | 66.71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 117.731 | α = 90 |
| b = 223.815 | β = 90 |
| c = 330.818 | 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 | 293 | PIXEL | CS-PAD CXI-1 | 1 micron KB mirror | 2014-11-28 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.7493 | SLAC LCLS | CXI |
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 | 3 | 43.12381 | 97.3 | 0.532 | 10.505 | 8.48 | 170444 | 61.0479099572 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 3 | 3.0517 | 88.8 | 2.257 | 2.91 | ||||||||||||||
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 | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0 | 3.00000997771 | 43.1230807017 | 1.32591484095 | 168044 | 1446 | 96.0284352606 | 0.264021318029 | 0.263691700807 | 0.303040832505 | Random selection w.r.t. complete reflections to 2 Angstroms | 47.3328786731 | |||||
| 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 | 18.9369033292 |
| f_angle_d | 0.487434134126 |
| f_chiral_restr | 0.0370617522078 |
| f_plane_restr | 0.00411381903435 |
| f_bond_d | 0.00191204375673 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 41612 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 124 |
| Heterogen Atoms | 8423 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| cctbx.xfel | data reduction |
| cctbx.prime | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
