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Structure of Recombinant Cytochrome ba3 Oxidase mutant A204F from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S8G PDB ENTRY 3S8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.5 293 50mM Sodium Cacodylate, 1.6M NaCl, 40% PEG400, pH 6.5, Lipidic Cubic Phase, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.55 α = 90 b = 98.21 β = 127.92 c = 94.86 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 100 CCD ADSC QUANTUM 315r 2011-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 74.83 98.34 34253 33684 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3S8G 2.5 74.83 34253 33684 1767 98.34 0.17174 0.16922 0.173 0.21969 0.2245 RANDOM 24.686
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] 0.87 1.96 -0.41 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_3_deg 16.768 r_dihedral_angle_4_deg 16.322 r_dihedral_angle_1_deg 6.672 r_scangle_it 4.014 r_scbond_it 2.602 r_angle_refined_deg 2.077 r_mcangle_it 1.648 r_mcbond_it 0.895 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_3_deg 16.768 r_dihedral_angle_4_deg 16.322 r_dihedral_angle_1_deg 6.672 r_scangle_it 4.014 r_scbond_it 2.602 r_angle_refined_deg 2.077 r_mcangle_it 1.648 r_mcbond_it 0.895 r_chiral_restr 0.145 r_bond_refined_d 0.022 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5828 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 456
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling