6DHF

RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KAF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.52980.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000
Crystal Properties
Matthews coefficientSolvent content
3.3763.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.817α = 90
b = 220.888β = 90
c = 307.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX170-HSCompound refractive lenses2016-07-14MSINGLE WAVELENGTH
31x-ray298CCDRAYONIX MX170-HSCompound refractive lenses2017-07-13MSINGLE WAVELENGTH
21x-ray298CCDRAYONIX MX170-HSCompound refractive lenses2016-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.305SLAC LCLSMFX
3FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.305SLAC LCLSMFX
2FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.305SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1401039.515
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
1114690

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0830.4399.960.97514.999211.04472399
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.082.11699.950.0130.53312.11

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5KAF2.0830.4271.33471189418299.740.18910.18850.247546.9236
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 AtomsNumber
Protein Atoms41576
Nucleic Acid Atoms
Solvent Atoms1882
Heterogen Atoms19173

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
PHASERphasing