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RT XFEL structure of Photosystem II 500 microseconds after the third illumination at 2.03 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RF1
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 3.21 61.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.534 α = 90 b = 222.832 β = 90 c = 309.505 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 MX340-HS 2021-07-01 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
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Drop-on-tape injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 20 7 9500 (KeV)
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Acoustic Droplet Ejection 4 (µl/min) undefined (µm) acoustic wave Aqueous buffer
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 2.03 31.23 99.92 0.99 3.83 105.5 519407 36.67
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) 1 2.03 2.06 0.09 0.36 9.1
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 FREE R-VALUE 7RF1 2.03 31.23 1.33 513905 4559 98.89 0.1996 0.1992 0.1995 0.2485 0.2482 41.85
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 Key Refinement Restraint Deviation f_dihedral_angle_d 17.6351 f_angle_d 1.1588 f_chiral_restr 0.0521 f_bond_d 0.0092 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41600 Nucleic Acid Atoms Solvent Atoms 1792 Heterogen Atoms 8546
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction cctbx.xfel data reduction cctbx.xfel.merge data scaling PHASER phasing