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RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DHE PDB entry 6DHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 0.1 M MES, pH 6.5, 0.1 M ammonium chloride, 35% w/v PEG5000
Crystal Properties Matthews coefficient Solvent content 3.17 61.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.018 α = 90 b = 221.781 β = 90 c = 308.191 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 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.30219 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
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 2.23 33.7 99.64 0.965 8 48.1 386505 39.13
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 2.23 2.27 0.056
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 PDB entry 6DHE 2.23 33.7 1.33 386314 3432 99.63 0.1728 0.1723 0.1733 0.2346 0.2359 46.65
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 21.5988 f_angle_d 1.5396 f_chiral_restr 0.0607 f_bond_d 0.0148 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47735 Nucleic Acid Atoms Solvent Atoms 1401 Heterogen Atoms 2486
Software Software Software Name Purpose PHENIX refinement cxi.merge data reduction PHASER phasing cxi.merge data scaling