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Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.3 293 100mM sodium cacodylate trihydrate pH 5.3, 37% PEG400, 1.4M NaCl
Room temperature for 2-3 days
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.85 α = 90 b = 100.32 β = 126.76 c = 96.62 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD MPCCD 2016-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.6314 SACLA BL3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (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 2.3 36.4 100 0.956 0.1937 3.74 14.7 1864107 50602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 0.366 1.2 14.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3S8F 2.3 36.4 47055 2511 99.92 0.1635 0.16174 0.19749 0.2166 RANDOM 51.446
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] -0.49 0.74 -1.19 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 20.854 r_dihedral_angle_3_deg 14.321 r_dihedral_angle_1_deg 5.876 r_long_range_B_refined 4.533 r_long_range_B_other 4.533 r_scangle_other 3.138 r_mcangle_it 2.515 r_mcangle_other 2.515 r_scbond_it 1.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 20.854 r_dihedral_angle_3_deg 14.321 r_dihedral_angle_1_deg 5.876 r_long_range_B_refined 4.533 r_long_range_B_other 4.533 r_scangle_other 3.138 r_mcangle_it 2.515 r_mcangle_other 2.515 r_scbond_it 1.932 r_scbond_other 1.932 r_angle_refined_deg 1.612 r_mcbond_it 1.596 r_mcbond_other 1.595 r_angle_other_deg 0.988 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5910 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling