8F4K
RT XFEL structure of the three-flash state of Photosystem II (3F, S0-rich) at 2.16 Angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7RF1 |
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 |
3.16 | 61.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.991 | α = 90 |
b = 221.755 | β = 90 |
c = 307.964 | 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 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 | 1.300 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | Drop-on-tape | injection |
Injection | |||||||
---|---|---|---|---|---|---|---|
Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
1 | Acoustic Droplet Ejection | 4 | acoustic wave | Aqueous buffer |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 40 | 20 | 7 | 9500 |
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 | 2.16 | 33.52 | 99.9 | 0.99 | 3.15 | 58.9 | 425199 | 40.58 |
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 | 2.16 | 2.19 | 0.05 | 0.39 | 9.3 |
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 | FREE R-VALUE | 7RF1 | 2.16 | 33.52 | 1.33 | 421849 | 3740 | 99.06 | 0.1856 | 0.1851 | 0.241 | 46.67 |
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 | 17.6793 |
f_angle_d | 1.1437 |
f_chiral_restr | 0.0531 |
f_bond_d | 0.0086 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 41600 |
Nucleic Acid Atoms | |
Solvent Atoms | 1609 |
Heterogen Atoms | 8566 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
cctbx.xfel | data reduction |
cctbx.xfel.merge | data scaling |
PHASER | phasing |