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Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus
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 6 285 5% PEG 1450, 20MM NACL, 10MM CACL2, 40MM MGSO4, 20MM MES BUFFER, PH 6.0, MICRO-BATCH METHOD UNDER OIL, TEMPERATURE 285K
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.25 α = 90 b = 228.43 β = 90 c = 287.12 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 PIXEL DECTRIS PILATUS3 6M 2016-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 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 19.99 99.5 0.087 0.998 13.7 6.8 459862
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 2.22 98.5 0.886 0.87 2.1 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WU2 2.1 19.99 438502 23043 99.31 0.1562 0.1541 0.1638 0.1966 0.2024 RANDOM 47.34
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] 0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.053 r_dihedral_angle_4_deg 17.601 r_dihedral_angle_3_deg 13.574 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 2.582 r_angle_other_deg 1.315 r_chiral_restr 0.12 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.053 r_dihedral_angle_4_deg 17.601 r_dihedral_angle_3_deg 13.574 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 2.582 r_angle_other_deg 1.315 r_chiral_restr 0.12 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 r_bond_other_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40940 Nucleic Acid Atoms Solvent Atoms 2356 Heterogen Atoms 10055
Software Software Software Name Purpose REFMAC refinement Coot model building PDB_EXTRACT data extraction MOLREP phasing XDS data reduction