8IRD

XFEL structure of cyanobacterial photosystem II following two flashes (2F) with a 20-nanosecond delay


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WS5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH62935.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER
Crystal Properties
Matthews coefficientSolvent content
3.5265.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.77α = 90
b = 231.76β = 90
c = 288.58γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDRAYONIX MX300-HS2020-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.24SACLABL2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.347.451000.9910.09449.7306.5370932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.340.5430.692

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE2.319.991.343709321865599.960.14440.14230.1835
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_d23.432
f_angle_d1.301
f_chiral_restr0.057
f_plane_restr0.009
f_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41493
Nucleic Acid Atoms
Solvent Atoms1823
Heterogen Atoms9317

Software

Software
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
cxi.mergedata scaling
PHASERphasing