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Crystal structure analysis of 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 Mes, NaCl, CaCl2, MgSO4, PEG 1450
Crystal Properties Matthews coefficient Solvent content 3.42 63.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.465 α = 90 b = 228.176 β = 90 c = 286.422 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 MX300HE 2015-07-22 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) 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 1.85 49 100 0.12 0.999 20.5 15.5 671082
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 1.85 1.95 100 1.5 1.9 15.4
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 1.85 19.99 636772 33616 99.9 0.16398 0.16203 0.1621 0.20073 0.2004 RANDOM 35.292
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 r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 16.042 r_dihedral_angle_3_deg 13.504 r_dihedral_angle_1_deg 5.923 r_angle_refined_deg 2.321 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 16.042 r_dihedral_angle_3_deg 13.504 r_dihedral_angle_1_deg 5.923 r_angle_refined_deg 2.321 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40661 Nucleic Acid Atoms Solvent Atoms 3925 Heterogen Atoms 9988
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing