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RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ARC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 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 3.42 64.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.19 α = 90 b = 228.51 β = 90 c = 286.4 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 2009-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 178.62 99.6 0.06 21.57 5.5 622012 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 99.7 0.773 2.63
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 3ARC 1.9 178.62 591655 31202 99.77 0.09516 0.09157 0.0933 0.1628 0.1639 RANDOM 39.479
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] 0.5 0.55 -1.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 63.088 r_dihedral_angle_2_deg 33.496 r_sphericity_bonded 26.094 r_dihedral_angle_4_deg 16.663 r_dihedral_angle_3_deg 13.188 r_scangle_other 9.515 r_long_range_B_refined 8.902 r_long_range_B_other 8.902 r_scbond_it 8.265 r_scbond_other 8.265
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 63.088 r_dihedral_angle_2_deg 33.496 r_sphericity_bonded 26.094 r_dihedral_angle_4_deg 16.663 r_dihedral_angle_3_deg 13.188 r_scangle_other 9.515 r_long_range_B_refined 8.902 r_long_range_B_other 8.902 r_scbond_it 8.265 r_scbond_other 8.265 r_mcangle_it 6 r_mcangle_other 6 r_dihedral_angle_1_deg 5.84 r_mcbond_it 5.07 r_mcbond_other 5.06 r_rigid_bond_restr 3.683 r_angle_refined_deg 3.27 r_angle_other_deg 1.138 r_chiral_restr 0.116 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.013 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41395 Nucleic Acid Atoms Solvent Atoms 3787 Heterogen Atoms 11954
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing