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Single-conformation model re-refinement of 2F/S3-rich PSII intermediate structure at 2.09 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 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 61.05
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 2019-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.30192 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 2.09 33.65 99.8 0.99 12.8 81 468019
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 2.13 0.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.09 33.65 466446 4162 99.837 0.1841 0.1835 0.1948 0.2433 0.2495 40.956
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] -1.49 -0.068 1.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.63 r_dihedral_angle_6_deg 16.676 r_dihedral_angle_3_deg 14.9 r_lrange_other 7.704 r_lrange_it 7.703 r_scangle_it 7.397 r_scangle_other 7.397 r_dihedral_angle_1_deg 6.817 r_scbond_it 6.228 r_scbond_other 6.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.63 r_dihedral_angle_6_deg 16.676 r_dihedral_angle_3_deg 14.9 r_lrange_other 7.704 r_lrange_it 7.703 r_scangle_it 7.397 r_scangle_other 7.397 r_dihedral_angle_1_deg 6.817 r_scbond_it 6.228 r_scbond_other 6.228 r_mcangle_it 5.903 r_mcangle_other 5.903 r_angle_refined_deg 5.191 r_mcbond_it 5.107 r_mcbond_other 5.106 r_angle_other_deg 1.215 r_chiral_restr 0.684 r_symmetry_nbd_refined 0.363 r_symmetry_xyhbond_nbd_refined 0.301 r_nbd_other 0.258 r_nbd_refined 0.242 r_symmetry_nbd_other 0.229 r_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.203 r_symmetry_xyhbond_nbd_other 0.129 r_symmetry_nbtor_other 0.098 r_gen_planes_other 0.04 r_bond_refined_d 0.027 r_metal_ion_refined 0.027 r_gen_planes_refined 0.021 r_dihedral_angle_other_2_deg 0.018 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41594 Nucleic Acid Atoms Solvent Atoms 1994 Heterogen Atoms 8608
Software Software Software Name Purpose REFMAC refinement cctbx.xfel data reduction cxi.merge data scaling PHASER phasing