5TIS

Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.5293Crystal 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 coefficientSolvent content
3.4664.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.87α = 90
b = 223.14β = 90
c = 310.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDRAYONIX MX170-HSCompound refractive lenses2015-11-18MSINGLE WAVELENGTH
21x-ray293CCDRAYONIX MX170-HSCompound refractive lenses2016-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE XPP1.3051SLAC LCLSXPP
2FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.3051SLAC LCLSMFX

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
12.2544.2899.980.97419.834158.4738554542.9839105609
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)
2.252.28999.980.0182.03610.37

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5KAI2.2500037156244.27662128221.32535968968385545342699.9333855190.1935501527370.1932149449280.230881600007Random selection w.r.t. complete reflections to 2 Angstroms47.7620084464
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.9024531457
f_angle_d0.503129489462
f_chiral_restr0.0382482334883
f_bond_d0.00571882994341
f_plane_restr0.00393061979526
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41719
Nucleic Acid Atoms
Solvent Atoms1179
Heterogen Atoms8659

Software

Software
Software NamePurpose
cctbx.xfeldata reduction
PHASERphasing
PHENIXrefinement