6DHE
RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5KAF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 6.5 | 298 | 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.4 | 63.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.906 | α = 90 |
b = 221.407 | β = 90 |
c = 308.668 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | CCD | RAYONIX MX170-HS | Compound refractive lenses | 2016-07-14 | M | SINGLE WAVELENGTH | |||||
3 | 1 | x-ray | 298 | CCD | RAYONIX MX170-HS | Compound refractive lenses | 2017-07-13 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 298 | CCD | RAYONIX MX170-HS | Compound refractive lenses | 2016-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.305 | SLAC LCLS | MFX |
3 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.305 | SLAC LCLS | MFX |
2 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.305 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | fixed target |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 40 | 10 | 3 | 9.515 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 157800 |
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 | 2.05 | 30.55 | 99.96 | 0.987 | 16.581 | 245.79 | 497372 | 33.09 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.05 | 2.085 | 99.95 | 0.018 | 0.53 | 12.58 |
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 | 5KAF | 2.05 | 30.552 | 1.33 | 496416 | 4403 | 99.8 | 0.1851 | 0.1846 | 0.2413 | 45.0801 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 41576 |
Nucleic Acid Atoms | |
Solvent Atoms | 1882 |
Heterogen Atoms | 19177 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
cctbx.xfel | data reduction |
PHASER | phasing |