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RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.09 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DHE
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 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.958 α = 90 b = 221.646 β = 90 c = 307.786 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 2018-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.30192 SLAC LCLS CXI
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 9 9.52 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Acoustic Droplet Ejection undefined (µl/min) undefined (µm) Acoustic Wave
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 2.09 33.65 99.8 0.979 12.8 81 468019 37.65
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 2.09 2.21 97.42 0.044 0.6
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 6DHE 2.09 33.65 1.33 465551 4128 99.26 0.1816 0.181 0.1811 0.2388 0.2376 45.46
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 18.0417 f_angle_d 1.462 f_chiral_restr 0.0605 f_bond_d 0.0145 f_plane_restr 0.0107
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41525 Nucleic Acid Atoms Solvent Atoms 1904 Heterogen Atoms 8582
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction cctbx.xfel data reduction PHASER phasing cxi.merge data scaling