6JLL

XFEL structure of cyanobacterial photosystem II (2F state, dataset1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6JLJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE298PEG, magnesium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.3563.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.97α = 90
b = 228.72β = 90
c = 286.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.2398SACLABL3

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target

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
12.15501000.997111337407701
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)
12.152.230.231

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 REPLACEMENTFREE R-VALUE6JLJ2.1519.991.35407701216231000.1580.1560.203
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_d22.958
f_angle_d1.389
f_chiral_restr0.05
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41513
Nucleic Acid Atoms
Solvent Atoms2577
Heterogen Atoms9672

Software

Software
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing