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Crystal structure of the PsbM-deletion mutant of photosystem II
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 PEG1450, sodium chloride, calcium chloride, magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.954 α = 90 b = 226.993 β = 90 c = 285.886 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 ADSC QUANTUM 210 2011-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.8 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.2 50 96.7 0.083 0.092 0.039 13.6 5.2 385629 385629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 96.6 0.705 0.705 0.788 0.344 1.1 4.9 55884
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 2.2 50 365283 19307 96.21 0.177 0.1744 0.1741 0.226 0.2253 RANDOM 42.025
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] 3 -0.89 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.984 r_dihedral_angle_4_deg 17.01 r_dihedral_angle_3_deg 14.763 r_dihedral_angle_1_deg 6.068 r_angle_refined_deg 2.335 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39962 Nucleic Acid Atoms Solvent Atoms 2370 Heterogen Atoms 9427
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction XSCALE data reduction MOLREP phasing