8F4J

RT XFEL structure of Photosystem II 4000 microseconds after the third illumination at 2.00 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7RF1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.52980.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000
Crystal Properties
Matthews coefficientSolvent content
3.261.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.339α = 90
b = 222.833β = 90
c = 309.192γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX300-HS2019-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.241SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Drop-on-tapeinjection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1Acoustic Droplet Ejection4acoustic waveAqueous buffer
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1102010000

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
1219.7499.90.994.22174.954313035.7
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)
122.030.030.3514.1

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-VALUE7RF1219.741.33537449477299.290.18230.18190.226340.71
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_d17.3552
f_angle_d1.1684
f_chiral_restr0.053
f_bond_d0.0091
f_plane_restr0.0079
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41600
Nucleic Acid Atoms
Solvent Atoms1905
Heterogen Atoms8566

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHASERphasing