5KAI

NH3-bound RT XFEL structure of Photosystem II 500 ms after the 2nd illumination (2F) at 2.8 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UB6PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0
experimental modelPDB 4PJ0PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.5293Crystal 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
3.7166.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.911α = 90
b = 224.268β = 90
c = 330.996γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD CXI-11 micron KB mirror2014-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.7492SLAC LCLSCXI

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
12.843.569812990.52411.6213.721340060.4069710515
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.848395.961.9354.17

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-VALUEPSII monomer composed of 4UB6 monomer and additional chain from 4PJ02.8000091477343.56981167741.32517238381211388179298.04183479430.2501573258620.2497335956010.299747309097Random selection w.r.t. complete reflections to 2 Angstroms56.5229924032
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_d21.0338406301
f_angle_d0.59701867629
f_chiral_restr0.0401636589989
f_plane_restr0.00478620789921
f_bond_d0.00308519133984
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41698
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms8476

Software

Software
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
PDB_EXTRACTdata extraction