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RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution
Serial Crystallography (SX)
Serial Crystallography (SX)
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 298 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000
Crystal Properties Matthews coefficient Solvent content 3.4 63.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.906 α = 90 b = 221.407 β = 90 c = 308.668 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX170-HS Compound refractive lenses 2016-07-14 M SINGLE WAVELENGTH 3 1 x-ray 298 CCD RAYONIX MX170-HS Compound refractive lenses 2017-07-13 M SINGLE WAVELENGTH 2 1 x-ray 298 CCD RAYONIX MX170-HS Compound refractive lenses 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.305 SLAC LCLS MFX 3 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.305 SLAC LCLS MFX 2 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.305 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 10 3 9.515 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.05 30.55 99.96 0.987 16.581 245.79 497372 33.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.085 99.95 0.018 0.53 12.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5KAF 2.05 30.552 1.33 496416 4403 99.8 0.1851 0.1846 0.1849 0.2413 0.2412 45.0801
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41576 Nucleic Acid Atoms Solvent Atoms 1882 Heterogen Atoms 19177
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction cctbx.xfel data reduction PHASER phasing