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Crystal structure of DBBQ-bound photosystem II complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.1 285 5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K
Crystal Properties Matthews coefficient Solvent content 3.33 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.185 α = 90 b = 228.462 β = 90 c = 286.626 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 100 CCD RAYONIX MX225HE 2021-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 99.2 0.072 0.999 14.2 5.4 460342 43.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 1.471 0.653 1.3
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 3wu2 2.1 49.02 1.34 459969 22959 99.2 0.159 0.1573 0.1628 0.1912 0.1943 59.3
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 24.9077 f_angle_d 1.2346 f_chiral_restr 0.0567 f_bond_d 0.0084 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41093 Nucleic Acid Atoms Solvent Atoms 2573 Heterogen Atoms 10357
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing Coot model building REFMAC refinement PHENIX refinement