6DHH
RT XFEL structure of Photosystem II 400 microseconds after the second illumination at 2.2 Angstrom resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
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 |
3.44 | 64.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.691 | α = 90 |
b = 222.529 | β = 90 |
c = 308.514 | 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 | 95.3 |
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 | 2.2 | 30.85 | 99.95 | 0.96 | 10.602 | 133.39 | 407641 |
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 | 2.2 | 2.238 | 99.99 | 0.006 | 0.707 | 13.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.2 | 30.851 | 1.33 | 406097 | 3606 | 99.61 | 0.1939 | 0.1933 | 0.2643 | 49.0838 |
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 | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 41576 |
Nucleic Acid Atoms | |
Solvent Atoms | 1881 |
Heterogen Atoms | 19175 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
cctbx.xfel | data reduction |
PHASER | phasing |