6W1T

RT XFEL structure of Photosystem II 250 microseconds after the second illumination at 2.01 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6DHEPDB entry 6DHE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2980.1 M MES, pH 6.5, 0.1 M ammonium chloride, 35% w/v PEG5000
Crystal Properties
Matthews coefficientSolvent content
3.1861.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.039α = 90
b = 221.917β = 90
c = 308.295γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2018-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.3027SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

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
12.0133.5999.780.97714.371.153567032.76
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)
12.012.030.051

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-VALUEPDB entry 6DHE2.0133.591.33527373468599.740.17570.17520.227839.79
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_d21.2795
f_angle_d1.5098
f_chiral_restr0.0628
f_bond_d0.0147
f_plane_restr0.0095
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms47711
Nucleic Acid Atoms
Solvent Atoms2081
Heterogen Atoms2510

Software

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