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RT XFEL structure of one-flash state of Photosystem II (1F, S2 rich) at 2.02 Angstrom
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 61.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.544 α = 90 b = 222.872 β = 90 c = 309.909 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 2018-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.300 SLAC LCLS MFX
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 2.02 30.14 99.87 0.99 17.273 187.62 527653 33.75
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 2.02 2.05 0.086
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.02 30.14 1.33 523697 4661 99.16 0.1735 0.173 0.1734 0.2251 0.2254 41.86
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 18.7827 f_angle_d 1.5096 f_chiral_restr 0.062 f_bond_d 0.0139 f_plane_restr 0.0119
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41515 Nucleic Acid Atoms Solvent Atoms 2055 Heterogen Atoms 8961
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction cctbx.xfel.merge data scaling PHENIX phasing